Novel methods of constructing libraries comprising displayed and/or expressed members of a diverse family of peptides, polypeptides or proteins and the novel libraries

ABSTRACT

Methods useful in constructing libraries that collectively display and/or express members of diverse families of peptides, polypeptides or proteins and the libraries produced using those methods. Methods of screening those libraries and the peptides, polypeptides or proteins identified by such screens.

This application is a divisional of U.S. patent application Ser. No.14/557,171, filed Dec. 1, 2014, now U.S. Pat. No. 9,683,028, issued Jun.20, 2017, which is a continuation of U.S. patent application Ser. No.13/464,047, filed May 4, 2012, now U.S. Pat. No. 8,901,045, issued Dec.2, 2014, which is a continuation of U.S. patent application Ser. No.10/045,674, filed Oct. 25, 2001, now U.S. Pat. No. 8,288,322, issuedOct. 16, 2012, which is a continuation-in-part of U.S. patentapplication Ser. No. 10/000,516, filed Oct. 24, 2001 (now abandoned),which is a continuation-in-part of U.S. patent application Ser. No.09/837,306, filed on Apr. 17, 2001 (abandoned), which claims the benefitfrom U.S. provisional application 60/198,069, filed Apr. 17, 2000. U.S.patent application Ser. No. 10/045,674, filed Oct. 25, 2001, now U.S.Pat. No. 8,288,322, issued Oct. 16, 2012, is also a continuation-in-partof U.S. patent application Ser. No. 09/837,306, filed on Apr. 17, 2001(now abandoned). All of the earlier applications are specificallyincorporated by reference herein.

The present invention relates to libraries of genetic packages thatdisplay and/or express a member of a diverse family of peptides,polypeptides or proteins and collectively display and/or express atleast a portion of the diversity of the family. In an alternativeembodiment, the invention relates to libraries that include a member ofa diverse family of peptides, polypeptides or proteins and collectivelycomprise at least a portion of the diversity of the family. In apreferred embodiment, the displayed and/or expressed polypeptides arehuman Fab.

More specifically, the invention is directed to the methods of cleavingsingle-stranded nucleic acids at chosen locations, the cleaved nucleicacids comprise at least a portion of the diversity of the family. In apreferred embodiment, the displayed and/or expressed polypeptides arehuman Fabs.

More specifically, the invention is directed to the methods of cleavingsingle-stranded nucleic acids at chosen locations, the cleaved nucleicacids encoding, at least in part, the peptides, polypeptides or proteinsdisplayed on the genetic packages of, and/or expressed in, the librariesof the invention. In a preferred embodiment, the genetic packages arefilamentous phage or phagemids or yeast.

The present invention further relates to vectors for displaying and/orexpressing a diverse family of peptides, polypeptides or proteins.

The present invention further relates to methods of screening thelibraries of the invention and to the peptides, polypeptides andproteins identified by such screening.

BACKGROUND OF THE INVENTION

It is now common practice in the art to prepare libraries of geneticpackages that display, express or comprise a member of a diverse familyof peptides, polypeptides or proteins and collectively display, expressor comprise at least a portion of the diversity of the family. In manycommon libraries, the peptides, polypeptides or proteins are related toantibodies. Often, they are Fabs or single chain antibodies.

In general, the DNAs that encode members of the families to be displayedand/or expressed must be amplified before they are cloned and used todisplay and/or express the desired member. Such amplification typicallymakes use of forward and backward primers.

Such primers can be complementary to sequences native to the DNA to beamplified or complementary to oligonucleotides attached at the 5′ or 3′ends of that DNA. Primers that are complementary to sequences native tothe DNA to be amplified are disadvantaged in that they bias the membersof the families to be displayed. Only those members that contain asequence in the native DNA that is substantially complementary to theprimer will be amplified. Those that do not will be absent from thefamily. For those members that are amplified, any diversity within theprimer region will be suppressed.

For example, in European patent 368,684 B1, the primer that is used isat the 5′ end of the V_(H) region of an antibody gene. It anneals to asequence region in the native DNA that is said to be “sufficiently wellconserved” within a single species. Such primer will bias the membersamplified to those having this “conserved” region. Any diversity withinthis region is extinguished.

It is generally accepted that human antibody genes arise through aprocess that involves a combinatorial selection of V and J or V, D, andJ followed by somatic mutations. Although most diversity occurs in theComplementary Determining Regions (CDRs), diversity also occurs in themore conserved Framework Regions (FRs) and at least some of thisdiversity confers or enhances specific binding to antigens (Ag). As aconsequence, libraries should contain as much of the CDR and FRdiversity as possible.

To clone the amplified DNAs of the peptides, polypeptides or proteinsthat they encode for display on a genetic package and/or for expression,the DNAs must be cleaved to produce appropriate ends for ligation to avector. Such cleavage is generally effected using restrictionendonuclease recognition sites carried on the primers. When the primersare at the 5′ end of DNA produced from reverse transcription of RNA,such restriction leaves deleterious 5′ untranslated regions in theamplified DNA. These regions interfere with expression of the clonedgenes and thus the display of the peptides, polypeptides and proteinscoded for by them.

SUMMARY OF THE INVENTION

It is an object of this invention to provide novel methods forconstructing libraries that display, express or comprise a member of adiverse family of peptides, polypeptides or proteins and collectivelydisplay, express or comprise at least a portion of the diversity of thefamily. These methods are not biased toward DNAs that contain nativesequences that are complementary to the primers used for amplification.They also enable any sequences that may be deleterious to expression tobe removed from the amplified DNA before cloning and displaying and/orexpressing.

It is another object of this invention to provide a method for cleavingsingle-stranded nucleic acid sequences at a desired location, the methodcomprising the steps of:

-   -   (i) contacting the nucleic acid with a single-stranded        oligonucleotide, the oligonucleotide being functionally        complementary to the nucleic acid in the region in which        cleavage is desired and including a sequence that with its        complement in the nucleic acid forms a restriction endonuclease        recognition site that on restriction results in cleavage of the        nucleic acid at the desired location; and    -   (ii) cleaving the nucleic acid solely at the recognition site        formed by the complementation of the nucleic acid and the        oligonucleotide;        the contacting and the cleaving steps being performed at a        temperature sufficient to maintain the nucleic acid in        substantially single-stranded form, the oligonucleotide being        functionally complementary to the nucleic acid over a large        enough region to allow the two strands to associate such that        cleavage may occur at the chosen temperature and at the desired        location, and the cleavage being carried out using a restriction        endonuclease that is active at the chosen temperature.

It is a further object of this invention to provide an alternativemethod for cleaving single-stranded nucleic acid sequences at a desiredlocation, the method comprising the steps of:

-   -   (i) contacting the nucleic acid with a partially double-stranded        oligonucleotide, the single-stranded region of the        oligonucleotide being functionally complementary to the nucleic        acid in the region in which cleavage is desired, and the        double-stranded region of the oligonucleotide having a        restriction endonuclease recognition site; and    -   (ii) cleaving the nucleic acid solely at the cleavage site        formed by the complementation of the nucleic acid and the        single-stranded region of the oligonucleotide;        the contacting and the cleaving steps being performed at a        temperature sufficient to maintain the nucleic acid in        substantially single-stranded form, the oligonucleotide being        functionally complementary to the nucleic acid over a large        enough region to allow the two strands to associate such that        cleavage may occur at the chosen temperature and at the desired        location, and the cleavage being carried out using a restriction        endonuclease that is active at the chosen temperature.

In an alternative embodiment of this object of the invention, therestriction endonuclease recognition site is not initially located inthe double-stranded part of the oligonucleotide. Instead, it is part ofan amplification primer, which primer is complementary to thedouble-stranded region of the oligonucleotide. On amplification of theDNA-partially double-stranded combination, the restriction endonucleaserecognition site carried on the primer becomes part of the DNA. It canthen be used to cleave the DNA.

Preferably, the restriction endonuclease recognition site is that of aType II-S restriction endonuclease whose cleavage site is located at aknown distance from its recognition site.

It is another object of the present invention to provide a method ofcapturing DNA molecules that comprise a member of a diverse family ofDNAs and collectively comprise at least a portion of the diversity ofthe family. These DNA molecules in single-stranded form have beencleaved by one of the methods of this invention. This method involvesligating the individual single-stranded DNA members of the family to apartially duplex DNA complex. The method comprises the steps of:

-   -   (i) contacting a single-stranded nucleic acid sequence that has        been cleaved with a restriction endonuclease with a partially        double-stranded oligonucleotide, the single-stranded region of        the oligonucleotide being functionally complementary to the        nucleic acid in the region that remains after cleavage, the        double-stranded region of the oligonucleotide including any        sequences necessary to return the sequences that remain after        cleavage into proper reading frame for expression and containing        a restriction endonuclease recognition site 5′ of those        sequences; and    -   (ii) cleaving the partially double-stranded oligonucleotide        sequence solely at the restriction endonuclease cleavage site        contained within the double-stranded region of the partially        double-stranded oligonucleotide.

As before, in this object of the invention, the restriction endonucleaserecognition site need not be located in the double-stranded portion ofthe oligonucleotide. Instead, it can be introduced on amplification withan amplification primer that is used to amplify the DNA-partiallydouble-stranded oligonucleotide combination.

It is another object of this invention to prepare libraries, thatdisplay, express or comprise a diverse family of peptides, polypeptidesor proteins and collectively display, express or comprise at least partof the diversity of the family, using the methods and DNAs describedabove.

It is an object of this invention to screen those libraries to identifyuseful peptides, polypeptides and proteins and to use those substancesin human therapy.

Additional objects of the invention are reflected in the originalclaims. Each of these claims is specifically incorporated by referencein this specification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of various methods that may be employed to amplifyVH genes without using primers specific for VH sequences. The T15oligonucleotide is shown in SEQ ID NO: 622.

FIG. 2 is a schematic of various methods that may be employed to amplifyVL genes without using primers specific for VL sequences.

FIG. 3 is a schematic of RACE amplification of antibody heavy and lightchains.

FIG. 4 depicts gel analysis of amplification products obtained after theprimary PCR reaction from 4 different patient samples.

FIG. 5 depicts gel analysis of cleaved kappa DNA from Example 2.

FIG. 6 depicts gel analysis of extender-cleaved kappa DNA from Example2.

FIG. 7 depicts gel analysis of the PCR product from the extender-kappaamplification from Example 2.

FIG. 8 depicts gel analysis of purified PCR product from theextender-kappa amplification from Example 2.

FIG. 9 depicts gel analysis of cleaved and ligated kappa light chainsfrom Example 2.

FIG. 10 is a schematic of the design for CDR1 and CDR2 syntheticdiversity (SEQ ID NOs: 636 and 637, respectively). The YADSVKG peptideis shown as SEQ ID NO: 604.

FIG. 11 is a schematic of the cloning schedule for construction of theheavy chain repertoire.

FIG. 12 is a schematic of the cleavage and ligation of the antibodylight chains. A: cleavage of the antibody light chains; B: ligation ofthe cleaved antibody light chains FIG. 13 depicts gel analysis ofcleaved and ligated lambda light chains from Example 4.

FIG. 14 is a schematic of the cleavage and ligation of the antibodyheavy chain. A:CJ cleavage of heavy chains; B: ligation of heavy chainCDR3 diversity.

FIG. 15 depicts gel analysis of cleaved and ligated lambda light chainsfrom Example 5.

FIG. 16 is a schematic of a phage display vector.

FIG. 17 is a schematic of a Fab cassette.

FIG. 18 is a schematic of a process for incorporating fixed FR1 residuesin an antibody lambda sequence. The PCRpr oligonucleotide is shown inSEQ ID NO: 605 while the Bridge oligonucleotide and encoded peptide areshown in SEQ ID NOs: 606-607, respectively.

FIG. 19 is a schematic of a process for incorporating fixed FR1 residuesin an antibody kappa sequence (see SEQ ID NOs: 608-611, respectively, inorder of appearance).

FIG. 20 is a schematic of a process for incorporating fixed FR1 residuesin an antibody heavy chain sequence. The PCRpr oligonucleotide is shownin SEQ ID NO: 612. The Bridge oligonucleotides are shown in SEQ ID NOs:613 and 615, respectively, in order of appearance, while the encodedpeptides are shown in SEQ ID NOs: 614 and 615, respectively, in order ofappearance.

TERMS

In this application, the following terms and abbreviations are used:

Sense strand The upper strand of ds DNA as usually written. In the sensestrand, 5′-ATG-3′ codes for Met. Antisense strand The lower strand of dsDNA as usually written. In the antisense strand, 3′-TAC-5′ wouldcorrespond to a Met codon in the sense strand. Forward primer A“forward” primer is complementary to a part of the sense strand andprimes for synthesis of a new antisense-strand molecule. “Forwardprimer” and “lower-strand primer” are equivalent. Backward primer A“backward” primer is complementary to a part of the antisense strand andprimes for synthesis of a new sense-strand molecule. “Backward primer”and “top-strand primer” are equivalent. Bases Bases are specified eitherby their position in a vector or gene as their position within a gene bycodon and base. For example, “89.1” is the first base of codon 89, 89.2is the second base of codon 89. Sv Streptavidin Ap Ampicillin ap^(R) Agene conferring ampicillin resistance. RERS Restriction endonucleaserecognition site RE Restriction endonuclease - cleaves preferentially atRERS URE Universal restriction endonuclease Functionally Two sequencesare sufficiently complementary so complementary as to anneal under thechosen conditions. AA Amino acid PCR Polymerization chain reaction GLGsGermline genes Ab Antibody: an immunoglobin. The term also covers anyprotein having a binding domain which is homologous to an immunoglobinbinding domain. A few examples of antibodies within this definition are,inter alia, immunoglobin isotypes and the Fab, F(ab¹)₂, scfv, Fv, dAband Fd fragments. Fab Two chain molecule comprising an Ab light chainand part of a heavy-chain. scFv A single-chain Ab comprising eitherVH::linker::VL or VL::linker::VH w.t. Wild type HC Heavy chain LC Lightchain VK A variable domain of a Kappa light chain. VH A variable domainof a heavy chain. VL A variable domain of a lambda light chain.

In this application when it is said that nucleic acids are cleavedsolely at the cleavage site of a restriction endonuclease, it should beunderstood that minor cleavage may occur at random, e.g., atnon-specific sites other than the specific cleavage site that ischaracteristic of the restriction endonuclease. The skilled worker willrecognize that such non-specific, random cleavage is the usualoccurrence. Accordingly, “solely at the cleavage site” of a restrictionendonuclease means that cleavage occurs preferentially at the sitecharacteristic of that endonuclease.

As used in this application and claims, the term “cleavage site formedby the complementation of the nucleic acid and the single-strandedregion of the oligonucleotide” includes cleavage sites formed by thesingle-stranded portion of the partially double-stranded oligonucleotideduplexing with the single-stranded DNA, cleavage sites in thedouble-stranded portion of the partially double-strandedoligonucleotide, and cleavage sites introduced by the amplificationprimer used to amplify the single-stranded DNA-partially double-strandedoligonucleotide combination.

In the two methods of this invention for preparing single-strandednucleic acid sequences, the first of those cleavage sites is preferred.In the methods of this invention for capturing diversity and cloning afamily of diverse nucleic acid sequences, the latter two cleavage sitesare preferred.

In this application, all references referred to are specificallyincorporated by reference.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The nucleic acid sequences that are useful in the methods of thisinvention, i.e., those that encode at least in part the individualpeptides, polypeptides and proteins displayed, or expressed in orcomprising the libraries of this invention, may be native, synthetic ora combination thereof. They may be mRNA, DNA or cDNA. In the preferredembodiment, the nucleic acids encode antibodies. Most preferably, theyencode Fabs.

The nucleic acids useful in this invention may be naturally diverse,synthetic diversity may be introduced into those naturally diversemembers, or the diversity may be entirely synthetic. For example,synthetic diversity can be introduced into one or more CDRs of antibodygenes. Preferably, it is introduced into CDR1 and CDR2 ofimmunoglobulins. Preferably, natural diversity is captured in the CDR3regions of the immunoglobin genes of this invention from B cells. Mostpreferably, the nucleic acids of this invention comprise a population ofimmunoglobin genes that comprise synthetic diversity in at least one,and more preferably both of the CDR1 and CDR2 and diversity in CDR3captured from B cells.

Synthetic diversity may be created, for example, through the use of TRIMtechnology (U.S. Pat. No. 5,869,644). TRIM technology allows controlover exactly which amino-acid types are allowed at variegated positionsand in what proportions. In TRIM technology, codons to be diversifiedare synthesized using mixtures of trinucleotides. This allows any set ofamino acid types to be included in any proportion.

Another alternative that may be used to generate diversified DNA ismixed oligonucleotide synthesis. With TRIM technology, one could allowAla and Trp. With mixed oligonucleotide synthesis, a mixture thatincluded Ala and Trp would also necessarily include Ser and Gly. Theamino-acid types allowed at the variegated positions are picked withreference to the structure of antibodies, or other peptides,polypeptides or proteins of the family, the observed diversity ingermline genes, the observed somatic mutations frequently observed, andthe desired areas and types of variegation.

In a preferred embodiment of this invention, the nucleic acid sequencesfor at least one CDR or other region of the peptides, polypeptides orproteins of the family are cDNAs produced by reverse transcription frommRNA. More preferably, the mRNAs are obtained from peripheral bloodcells, bone marrow cells, spleen cells or lymph node cells (such asB-lymphocytes or plasma cells) that express members of naturally diversesets of related genes. More preferable, the mRNAs encode a diversefamily of antibodies. Most preferably, the mRNAs are obtained frompatients suffering from at least one autoimmune disorder or cancer.Preferably, mRNAs containing a high diversity of autoimmune diseases,such as systemic lupus erythematosus, systemic sclerosis, rheumatoidarthritis, antiphospholipid syndrome and vasculitis are used.

In a preferred embodiment of this invention, the cDNAs are produced fromthe mRNAs using reverse transcription. In this preferred embodiment, themRNAs are separated from the cell and degraded using standard methods,such that only the full length (i.e., capped) mRNAs remain. The cap isthen removed and reverse transcription used to produce the cDNAs.

The reverse transcription of the first (antisense) strand can be done inany manner with any suitable primer. See, e.g., HJ de Haard et al.,Journal of Biological Chemistry, 274(26):18218-30 (1999). In thepreferred embodiment of this invention where the mRNAs encodeantibodies, primers that are complementary to the constant regions ofantibody genes may be used. Those primers are useful because they do notgenerate bias toward subclasses of antibodies. In another embodiment,poly-dT primers may be used (and may be preferred for the heavy-chaingenes). Alternatively, sequences complementary to the primer may beattached to the termini of the antisense strand.

In one preferred embodiment of this invention, the reverse transcriptaseprimer may be biotinylated, thus allowing the cDNA product to beimmobilized on streptavidin (Sv) beads. Immobilization can also beeffected using a primer labeled at the 5′ end with one of a) free aminegroup, b) thiol, c) carboxylic acid, or d) another group not found inDNA that can react to form a strong bond to a known partner on aninsoluble medium. If, for example, a free amine (preferably primaryamine) is provided at the 5′ end of a DNA primer, this amine can bereacted with carboxylic acid groups on a polymer bead using standardamide-forming chemistry. If such preferred immobilization is used duringreverse transcription, the top strand RNA is degraded using well-knownenzymes, such as a combination of RNAseH and RNAseA, either before orafter immobilization.

The nucleic acid sequences useful in the methods of this invention aregenerally amplified before being used to display and/or express thepeptides, polypeptides or proteins that they encode. Prior toamplification, the single-stranded DNAs may be cleaved using either ofthe methods described before. Alternatively, the single-stranded DNAsmay be amplified and then cleaved using one of those methods.

Any of the well known methods for amplifying nucleic acid sequences maybe used for such amplification. Methods that maximize, and do not bias,diversity are preferred. In a preferred embodiment of this inventionwhere the nucleic acid sequences are derived from antibody genes, thepresent invention preferably utilizes primers in the constant regions ofthe heavy and light chain genes and primers to a synthetic sequence thatare attached at the 5′ end of the sense strand. Priming at suchsynthetic sequence avoids the use of sequences within the variableregions of the antibody genes. Those variable region priming sitesgenerate bias against V genes that are either of rare subclasses or thathave been mutated at the priming sites. This bias is partly due tosuppression of diversity within the primer region and partly due to lackof priming when many mutations are present in the region complementaryto the primer. The methods disclosed in this invention have theadvantage of not biasing the population of amplified antibody genes forparticular V gene types.

The synthetic sequences may be attached to the 5′ end of the DNA strandby various methods well known for ligating DNA sequences together. RTCapExtention is one preferred method.

In RT CapExtention (derived from Smart PCR™), a short overlap (5′- . . .GGG-3′ in the upper-strand primer (USP-GGG) complements 3′-CCC . . . 5′in the lower strand) and reverse transcriptases are used so that thereverse complement of the upper-strand primer is attached to the lowerstrand.

FIGS. 1 and 2 show schematics to amplify VH and VL genes using RTCapExtention. FIG. 1 shows a schematic of the amplification of VH genes.FIG. 1, Panel A shows a primer specific to the poly-dT region of the 3′UTR priming synthesis of the first, lower strand. Primers that bind inthe constant region are also suitable. Panel B shows the lower strandextended at its 3′ end by three Cs that are not complementary to themRNA. Panel C shows the result of annealing a synthetic top-strandprimer ending in three GGGs that hybridize to the 3′ terminal CCCs andextending the reverse transcription extending the lower strand by thereverse complement of the synthetic primer sequence. Panel D shows theresult of PCR amplification using a 5′ biotinylated synthetic top-strandprimer that replicates the 5′ end of the synthetic primer of panel C anda bottom-strand primer complementary to part of the constant domain.Panel E shows immobilized double-stranded (ds) cDNA obtained by using a5′-biotinylated top-strand primer.

FIG. 2 shows a similar schematic for amplification of VL genes. FIG. 2,Panel A shows a primer specific to the constant region at or near the 3′end priming synthesis of the first, lower strand. Primers that bind inthe poly-dT region are also suitable. Panel B shows the lower strandextended at its 3′ end by three Cs that are not complementary to themRNA. Panel C shows the result of annealing a synthetic top-strandprimer ending in three GGGs that hybridize to the 3′ terminal CCCs andextending the reverse transcription extending the lower strand by thereverse complement of the synthetic primer sequence. Panel D shows theresult of PCR amplification using a 5′ biotinylated synthetic top-strandprimer that replicates the 5′ end of the synthetic primer of panel C anda bottom-strand primer complementary to part of the constant domain. Thebottom-strand primer also contains a useful restriction endonucleasesite, such as AscI. Panel E shows immobilized ds cDNA obtained by usinga 5′-biotinylated top-strand primer.

In FIGS. 1 and 2, each V gene consists of a 5′ untranslated region (UTR)and a secretion signal, followed by the variable region, followed by aconstant region, followed by a 3′ untranslated region (which typicallyends in poly-A). An initial primer for reverse transcription may becomplementary to the constant region or to the poly A segment of the3′-UTR. For human heavy-chain genes, a primer of 15 T is preferred.Reverse transcriptases attach several C residues to the 3′ end of thenewly synthesized DNA. RT CapExtention exploits this feature. Thereverse transcription reaction is first run with only a lower-strandprimer. After about 1 hour, a primer ending in GGG (USP-GGG) and moreRTase are added. This causes the lower-strand cDNA to be extended by thereverse complement of the USP-GGG up to the final GGG. Using one primeridentical to part of the attached synthetic sequence and a second primercomplementary to a region of known sequence at the 3′ end of the sensestrand, all the V genes are amplified irrespective of their V genesubclass.

In another preferred embodiment, synthetic sequences may be added byRapid Amplification of cDNA Ends (RACE) (see Frohman, M. A., Dush, M.K., & Martin, G. R. (1988) Proc. Natl. Acad. Sci. USA (85): 8998-900?).

FIG. 1 shows a schematic of RACE amplification of antibody heavy andlight chains. First, mRNA is selected by treating total or poly(A+) RNAwith calf intestinal phosphatase (CIP) to remove the 5′-phosphate fromall molecules that have them such as ribosomal RNA, fragmented mRNA,tRNA and genomic DNA. Full length mRNA (containing a protective 7-methylcap structure) is uneffected. The RNA is then treated with tobacco acidpyrophosphatase (TAP) to remove the cap structure from full length mRNAsleaving a 5′-monophosphate group. Next, a synthetic RNA adaptor isligated to the RNA population, only molecules which have a 5-phosphate(uncapped, full length mRNAs) will accept the adaptor. Reversetrascriptase reactions using an oligodT primer, and nested PCR (usingone adaptor primer (located in the 5′ synthetic adaptor) and one primerfor the gene) are then used to amplify the desired transcript.

In a preferred embodiment of this invention, the upper strand or lowerstrand primer may be also biotinylated or labeled at the 5′ end with oneof a) free amino group, b) thiol, c) carboxylic acid and d) anothergroup not found in DNA that can react to form a strong bond to a knownpartner as an insoluble medium. These can then be used to immobilize thelabeled strand after amplification. The immobilized DNA can be eithersingle or double-stranded.

After amplification (using e.g., RT CapExtension or RACE), the DNAs ofthis invention are rendered single-stranded. For example, the strandscan be separated by using a biotinylated primer, capturing thebiotinylated product on streptavidin beads, denaturing the DNA, andwashing away the complementary strand. Depending on which end of thecaptured DNA is wanted, one will choose to immobilize either the upper(sense) strand or the lower (antisense) strand.

To prepare the single-stranded amplified DNAs for cloning into geneticpackages so as to effect display of, or for expression of, the peptides,polypeptides or proteins encoded, at least in part, by those DNAs, theymust be manipulated to provide ends suitable for cloning and displayand/or expression. In particular, any 5′ untranslated regions andmammalian signal sequences must be removed and replaced, in frame, by asuitable signal sequence that functions in the display or expressionhost. Additionally, parts of the variable domains (in antibody genes)may be removed and replaced by synthetic segments containing syntheticdiversity. The diversity of other gene families may likewise be expandedwith synthetic diversity.

According to the methods of this invention, there are two ways tomanipulate the single-stranded DNAs for display and/or expression. Thefirst method comprises the steps of:

-   -   (i) contacting the nucleic acid with a single-stranded        oligonucleotide, the oligonucleotide being functionally        complementary to the nucleic acid in the region in which        cleavage is desired and including a sequence that with its        complement in the nucleic acid forms a restriction endonuclease        recognition site that on restriction results in cleavage of the        nucleic acid at the desired location; and    -   (ii) cleaving the nucleic acid solely at the recognition site        formed by the complementation of the nucleic acid and the        oligonucleotide;        the contacting and the cleaving steps being performed at a        temperature sufficient to maintain the nucleic acid in        substantially single-stranded form, the oligonucleotide being        functionally complementary to the nucleic acid over a large        enough region to allow the two strands to associate such that        cleavage may occur at the chosen temperature and at the desired        location, and the cleavage being carried out using a restriction        endonuclease that is active at the chosen temperature.

In this first method, short oligonucleotides are annealed to thesingle-stranded DNA so that restriction endonuclease recognition sitesformed within the now locally double-stranded regions of the DNA can becleaved. In particular, a recognition site that occurs at the sameposition in a substantial fraction of the single-stranded DNAs isidentical.

For antibody genes, this can be done using a catalog of germlinesequences. See, e.g.,“www.mrc-cpe.cam.ac.uk/imt-doc/restricted/ok.html.” Updates can beobtained from this site under the heading “Amino acid and nucleotidesequence alignments.” For other families, similar comparisons exist andmay be used to select appropriate regions for cleavage and to maintaindiversity.

For example, Table 1 depicts the DNA sequences of the FR3 regions of the51 known human VH germline genes. In this region, the genes containrestriction endonuclease recognition sites shown in Table 2. Restrictionendonucleases that cleave a large fraction of germline genes at the samesite are preferred over endonucleases that cut at a variety of sites.Furthermore, it is preferred that there be only one site for therestriction endonucleases within the region to which the shortoligonucleotide binds on the single-stranded DNA, e.g., about 10 baseson either side of the restriction endonuclease recognition site.

An enzyme that cleaves downstream in FR3 is also more preferable becauseit captures fewer mutations in the framework. This may be advantageousis some cases. However, it is well known that framework mutations existand confer and enhance antibody binding. The present invention, bychoice of appropriate restriction site, allows all or part of FR3diversity to be captured. Hence, the method also allows extensivediversity to be captured.

Finally, in the methods of this invention restriction endonucleases thatare active between about 37° C. and about 75° C. are used. Preferably,restriction endonucleases that are active between about 45° C. and about75° C. may be used. More preferably, enzymes that are active above 50°C., and most preferably active about 55° C., are used. Such temperaturesmaintain the nucleic acid sequence to be cleaved in substantiallysingle-stranded form.

Enzymes shown in Table 2 that cut many of the heavy chain FR3 germlinegenes at a single position include: MaeIII(24@4), Tsp45I(21@4),HphI(44@5), BsaJI(23@65), AluI(23@47), BlpI(21@48), DdeI(29@58),BglII(10@61), MslI(44@72), BsiEI(23@74), EaeI(23@74), EagI(23@74),HaeIII(25@75), Bst4CI(51@86), HpyCH4III(51@86), HinfI(38@2), MlyI(18@2),PleI(18@2), MnlI(31@67), HpyCH4V(21@44), BsmAI(16@11), BpmI(19@12),XmnI(12@30), and SacI(11@51). (The notation used means, for example,that BsmAI cuts 16 of the FR3 germline genes with a restrictionendonuclease recognition site beginning at base 11 of FR3.)

For cleavage of human heavy chains in FR3, the preferred restrictionendonucleases are: Bst4CI (or TaaI or HpyCH4III), BipI, HpyCH4V, andMslI. Because ACNGT (the restriction endonuclease recognition site forBst4CI, TaaI, and HpyCH4III) is found at a consistent site in all thehuman FR3 germline genes, one of those enzymes is the most preferred forcapture of heavy chain CDR3 diversity. BlpI and HpyCH4V arecomplementary. BlpI cuts most members of the VH1 and VH4 families whileHpyCH4V cuts most members of the VH3, VH5, VH6, and VH7 families.Neither enzyme cuts VH2s, but this is a very small family, containingonly three members. Thus, these enzymes may also be used in preferredembodiments of the methods of this invention.

The restriction endonucleases HpyCH4III, Bst4CI, and TaaI all recognize5′-ACnGT-3′ and cut upper strand DNA after n and lower strand DNA beforethe base complementary to n. This is the most preferred restrictionendonuclease recognition site for this method on human heavy chainsbecause it is found in all germline genes. Furthermore, the restrictionendonuclease recognition region (ACnGT) matches the second and thirdbases of a tyrosine codon (tay) and the following cysteine codon (tgy)as shown in Table 3. These codons are highly conserved, especially thecysteine in mature antibody genes.

Table 4 E shows the distinct oligonucleotides of length 22 (except thelast one which is of length 20) bases. Table 5 C shows the analysis of1617 actual heavy chain antibody genes. Of these, 1511 have the site andmatch one of the candidate oligonucleotides to within 4 mismatches.Eight oligonucleotides account for most of the matches and are given inTable 4 F.1. The 8 oligonucleotides are very similar so that it islikely that satisfactory cleavage will be achieved with only oneoligonucleotide (such as H43.77.97.1-02#1) by adjusting temperature, pH,salinity, and the like. One or two oligonucleotides may likewise sufficewhenever the germline gene sequences differ very little and especiallyif they differ very little close to the restriction endonucleaserecognition region to be cleaved. Table 5 D shows a repeat analysis of1617 actual heavy chain antibody genes using only the 8 chosenoligonucleotides. This shows that 1463 of the sequences match at leastone of the oligonucleotides to within 4 mismatches and have the site asexpected. Only 7 sequences have a second HpyCH4III restrictionendonuclease recognition region in this region.

Another illustration of choosing an appropriate restriction endonucleaserecognition site involves cleavage in FR1 of human heavy chains.Cleavage in FR1 allows capture of the entire CDR diversity of the heavychain.

The germline genes for human heavy chain FR1 are shown in Table 6. Table7 shows the restriction endonuclease recognition sites found in humangermline genes FR1s. The preferred sites are BsgI(GTGCAG;39@4),BsoFI(GCngc;43@6,11@9,2@3,1@12), TseI(Gcwgc;43@6,11@9,2@3,1@12),MspAlI(CMGckg;46@7,2@1), PvuII(CAGctg;46@7,2@1), AluI(AGct;48@82@2),DdcI(Ctnag;22@52,9@48), HphI(tcacc;22@80), BssKI(Nccngg;35@39,2@40),BsaJI(Ccnngg;32@40,2@41), BstNI(CCwgg;33@40), ScrFI(CCngg;35@40,2@41),EcoO109I(RGgnccy;22@46, 11@43), Sau96I(Ggncc;23@47,11@44),AvaII(Ggwcc;23@47,4@44), PpuMI(RGgwccy;22@46,4@43), BsmFI(gtccc;20@48),HinfI(Gantc;34@16,21@56,21@77), TriI(21@77), MlyI(GAGTC;34@16),MlyI(gactc;21@5b6), and AlwNI(CAGnnnctg;22@68). The more preferred sitesare MspAI and PvuII. MspAI and PvuII have 46 sites at 7-12 and 2 at 1-6.To avoid cleavage at both sites, oligonucleotides are used that do notfully cover the site at 1-6. Thus, the DNA will not be cleaved at thatsite. We have shown that DNA that extends 3, 4, or 5 bases beyond aPvuII-site can be cleaved efficiently.

Another illustration of choosing an appropriate restriction endonucleaserecognition site involves cleavage in FR1 of human kappa light chains.Table 8 shows the human kappa FR1 germline genes and Table 9 showsrestriction endonuclease recognition sites that are found in asubstantial number of human kappa FR1 germline genes at consistentlocations. Of the restriction endonuclease recognition sites listed,BsmAI and PflFI are the most preferred enzymes. BsmAI sites are found atbase 18 in 35 of 40 germline genes. PflFI sites are found in 35 of 40germline genes at base 12.

Another example of choosing an appropriate restriction endonucleaserecognition site involves cleavage in FR1 of the human lambda lightchain. Table 10 shows the 31 known human lambda FR1 germline genesequences. Table 11 shows restriction endonuclease recognition sitesfound in human lambda FR1 germline genes. HinfI and DdeI are the mostpreferred restriction endonucleases for cutting human lambda chains inFR1.

After the appropriate site or sites for cleavage are chosen, one or moreshort oligonucleotides are prepared so as to functionally complement,alone or in combination, the chosen recognition site. Theoligonucleotides also include sequences that flank the recognition sitein the majority of the amplified genes. This flanking region allows thesequence to anneal to the single-stranded DNA sufficiently to allowcleavage by the restriction endonuclease specific for the site chosen.

The actual length and sequence of the oligonucleotide depends on therecognition site and the conditions to be used for contacting andcleavage. The length must be sufficient so that the oligonucleotide isfunctionally complementary to the single-stranded DNA over a largeenough region to allow the two strands to associate such that cleavagemay occur at the chosen temperature and at the desired location.

Typically, the oligonucleotides of this preferred method of theinvention are about 17 to about 30 nucleotides in length. Below about 17bases, annealing is too weak and above 30 bases there can be a loss ofspecificity. A preferred length is 18 to 24 bases.

Oligonucleotides of this length need not be identical complements of thegermline genes. Rather, a few mismatches taken may be tolerated.Preferably, however, no more than 1-3 mismatches are allowed. Suchmismatches do not adversely affect annealing of the oligonucleotide tothe single-stranded DNA. Hence, the two DNAs are said to be functionallycomplementary.

The second method to manipulate the single-stranded DNAs of thisinvention for display and/or expression comprises the steps of:

-   -   (i) contacting the nucleic acid with a partially double-stranded        oligonucleotide, the single-stranded region of the        oligonucleotide being functionally complementary to the nucleic        acid in the region in which cleavage is desired, and the        double-stranded region of the oligonucleotide having a        restriction endonuclease recognition site; and    -   (ii) cleaving the nucleic acid solely at the cleavage site        formed by the complementation of the nucleic acid and the        single-stranded region of the oligonucleotide;        the contacting and the cleaving steps being performed at a        temperature sufficient to maintain the nucleic acid in        substantially single-stranded form, the oligonucleotide being        functionally complementary to the nucleic acid over a large        enough region to allow the two strands to associate such that        cleavage may occur at the chosen temperature and at the desired        location, and the cleavage being carried out using a restriction        endonuclease that is active at the chosen temperature.

As explained above, the cleavage site may be formed by thesingle-stranded portion of the partially double-stranded oligonucleotideduplexing with the single-stranded DNA, the cleavage site may be carriedin the double-stranded portion of the partially double-strandedoligonucleotide, or the cleavage site may be introduced by theamplification primer used to amplify the single-stranded DNA-partiallydouble-stranded oligonucleotide combination. In this embodiment, thefirst is preferred. And, the restriction endonuclease recognition sitemay be located in either the double-stranded portion of theoligonucleotide or introduced by the amplification primer, which iscomplementary to that double-stranded region, as used to amplify thecombination.

Preferably, the restriction endonuclease site is that of a Type II-Srestriction endonuclease, whose cleavage site is located at a knowndistance from its recognition site.

This second method, preferably, employs Universal RestrictionEndonucleases (“URE”). UREs are partially double-strandedoligonucleotides. The single-stranded portion or overlap of the UREconsists of a DNA adapter that is functionally complementary to thesequence to be cleaved in the single-stranded DNA. The double-strandedportion consists of a restriction endonuclease recognition site,preferably type II-S.

The URE method of this invention is specific and precise and cantolerate some (e.g., 1-3) mismatches in the complementary regions, i.e.,it is functionally complementary to that region. Further, conditionsunder which the URE is used can be adjusted so that most of the genesthat are amplified can be cut, reducing bias in the library producedfrom those genes.

The sequence of the single-stranded DNA adapter or overlap portion ofthe URE typically consists of about 14-22 bases. However, longer orshorter adapters may be used. The size depends on the ability of theadapter to associate with its functional complement in thesingle-stranded DNA and the temperature used for contacting the URE andthe single-stranded DNA at the temperature used for cleaving the DNAwith the restriction enzyme. The adapter must be functionallycomplementary to the single-stranded DNA over a large enough region toallow the two strands to associate such that the cleavage may occur atthe chosen temperature and at the desired location. We prefersinge-stranded or overlap portions of 14-17 bases in length, and morepreferably 18-20 bases in length.

The site chosen for cleavage using the URE is preferably one that issubstantially conserved in the family of amplified DNAs. As compared tothe first cleavage method of this invention, these sites do not need tobe endonuclease recognition sites. However, like the first method, thesites chosen can be synthetic rather than existing in the native DNA.Such sites may be chosen by references to the sequences of knownantibodies or other families of genes. For example, the sequences ofmany germline genes are reported atwww.mrc-cpe.cam.ac.uk/imt-doc/restricted/ok.html. For example, onepreferred site occurs near the end of FR3—codon 89 through the secondbase of codon 93. CDR3 begins at codon 95.

The sequences of 79 human heavy-chain genes are also available atwww.ncbi.nlm.nih.gov/entre2/nucleotide.html. This site can be used toidentify appropriate sequences for URE cleavage according to the methodsof this invention. See, e.g., Table 12B.

Most preferably, one or more sequences are identified using these sitesor other available sequence information. These sequences together arepresent in a substantial fraction of the amplified DNAs. For example,multiple sequences could be used to allow for known diversity ingermline genes or for frequent somatic mutations. Synthetic degeneratesequences could also be used. Preferably, a sequence(s) that occurs inat least 65% of genes examined with no more than 2-3 mismatches ischosen

URE single-stranded adapters or overlaps are then made to becomplementary to the chosen regions. Conditions for using the UREs aredetermined empirically. These conditions should allow cleavage of DNAthat contains the functionally complementary sequences with no more than2 or 3 mismatches but that do not allow cleavage of DNA lacking suchsequences.

As described above, the double-stranded portion of the URE includes anendonuclease recognition site, preferably a Type II-S recognition site.Any enzyme that is active at a temperature necessary to maintain thesingle-stranded DNA substantially in that form and to allow thesingle-stranded DNA adapter portion of the URE to anneal long enough tothe single-stranded DNA to permit cleavage at the desired site may beused.

The preferred Type II-S enzymes for use in the URE methods of thisinvention provide asymmetrical cleavage of the single-stranded DNA.Among these are the enzymes listed in Table 13. The most preferred TypeII-S enzyme is FokI.

When the preferred FokI containing URE is used, several conditions arepreferably used to effect cleavage:

-   -   1) Excess of the URE over target DNA should be present to        activate the enzyme. URE present only in equimolar amounts to        the target DNA would yield poor cleavage of ssDNA because the        amount of active enzyme available would be limiting.    -   2) An activator may be used to activate part of the FokI enzyme        to dimerize without causing cleavage. Examples of appropriate        activators are shown in Table 14.    -   3) The cleavage reaction is performed at a temperature between        45°−75° C., preferably above 50° C. and most preferably above        55° C.

The UREs used in the prior art contained a 14-base single-strandedsegment, a 10-base stem (containing a FokI site), followed by thepalindrome of the 10-base stem. While such UREs may be used in themethods of this invention, the preferred UREs of this invention alsoinclude a segment of three to eight bases (a loop) between the FokIrestriction endonuclease recognition site containing segments. In thepreferred embodiment, the stem (containing the FokI site) and itspalindrome are also longer than 10 bases. Preferably, they are 10-14bases in length. Examples of these “lollipop” URE adapters are shown inTable 15.

One example of using a URE to cleave an single-stranded DNA involves theFR3 region of human heavy chain. Table 16 shows an analysis of 840full-length mature human heavy chains with the URE recognition sequencesshown. The vast majority (718/840=0.85) will be recognized with 2 orfewer mismatches using five UREs (VHS881-1.1, VHS881-1.2, VH3081-2.1,VHS861-4.1, and VHS601-9.1). Each has a 20-base adaptor sequence tocomplement the germline gene, a ten-base stem segment containing a FokIsite, a five base loop, and the reverse complement of the first stemsegment. Annealing those adapters, alone or in combination, tosingle-stranded antisense heavy chain DNA and treating with FokI in thepresence of, e.g., the activator FOKIact, will lead to cleavage of theantisense strand at the position indicated.

Another example of using a URE(s) to cleave a single-stranded DNAinvolves the FR1 region of the human Kappa light chains. Table 17 showsan analysis of 182 full-length human kappa chains for matching by thefour 19-base probe sequences shown. Ninety-six percent of the sequencesmatch one of the probes with 2 or fewer mismatches. The URE adaptersshown in Table 17 are for cleavage of the sense strand of kappa chains.Thus, the adaptor sequences are the reverse complement of the germlinegene sequences. The URE consists of a ten-base stem, a five base loop,the reverse complement of the stem and the complementation sequence. Theloop shown here is TTCTT, but other sequences could be used. Itsfunction is to interrupt the palindrome of the stems so that formationof a lollypop monomer is favored over dimerization. Table 17 also showswhere the sense strand is cleaved.

Another example of using a URE to cleave a single-stranded DNA involvesthe human lambda light chain. Table 18 shows analysis of 128 humanlambda light chains for matching the four 19-base probes shown. Withthree or fewer mismatches, 88 of 128 (69%) of the chains match one ofthe probes. Table 18 also shows URE adapters corresponding to theseprobes. Annealing these adapters to upper-strand ssDNA of lambda chainsand treatment with FokI in the presence of FOKIact at a temperature ator above 45° C. will lead to specific and precise cleavage of thechains.

The conditions under which the short oligonucleotide sequences of thefirst method and the UREs of the second method are contacted with thesingle-stranded DNAs may be empirically determined. The conditions mustbe such that the single-stranded DNA remains in substantiallysingle-stranded form. More particularly, the conditions must be suchthat the single-stranded DNA does not form loops that may interfere withits association with the oligonucleotide sequence or the URE or that maythemselves provide sites for cleavage by the chosen restrictionendonuclease.

The effectiveness and specificity of short oligonucleotides (firstmethod) and UREs (second method) can be adjusted by controlling theconcentrations of the URE adapters/oligonucleotides and substrate DNA,the temperature, the pH, the concentration of metal ions, the ionicstrength, the concentration of chaotropes (such as urea and formamide),the concentration of the restriction endonuclease (e.g., FokI), and thetime of the digestion. These conditions can be optimized with syntheticoligonucleotides having: 1) target germline gene sequences, 2) mutatedtarget gene sequences, or 3) somewhat related non-target sequences. Thegoal is to cleave most of the target sequences and minimal amounts ofnon-targets.

In accordance with this invention, the single-stranded DNA is maintainedin substantially that form using a temperature between about 37° C. andabout 75° C. Preferably, a temperature between about 45° C. and about75° C. is used. More preferably, a temperature between 50° C. and 60°C., most preferably between 55° C. and 60° C., is used. Thesetemperatures are employed both when contacting the DNA with theoligonucleotide or URE and when cleaving the DNA using the methods ofthis invention.

The two cleavage methods of this invention have several advantages. Thefirst method allows the individual members of the family ofsingle-stranded DNAs to be cleaved preferentially at one substantiallyconserved endonuclease recognition site. The method also does notrequire an endonuclease recognition site to be built into the reversetranscription or amplification primers. Any native or synthetic site inthe family can be used.

The second method has both of these advantages. In addition, thepreferred URE method allows the single-stranded DNAs to be cleaved atpositions where no endonuclease recognition site naturally occurs or hasbeen synthetically constructed.

Most importantly, both cleavage methods permit the use of 5′ and 3′primers so as to maximize diversity and then cleavage to remove unwantedor deleterious sequences before cloning, display and/or expression.

After cleavage of the amplified DNAs using one of the methods of thisinvention, the DNA is prepared for cloning, display and/or expression.This is done by using a partially duplexed synthetic DNA adapter, whoseterminal sequence is based on the specific cleavage site at which theamplified DNA has been cleaved.

The synthetic DNA is designed such that when it is ligated to thecleaved single-stranded DNA in proper reading frame so that the desiredpeptide, polypeptide or protein can be displayed on the surface of thegenetic package and/or expressed. Preferably, the double-strandedportion of the adapter comprises the sequence of several codons thatencode the amino acid sequence characteristic of the family of peptides,polypeptides or proteins up to the cleavage site. For human heavychains, the amino acids of the 3-23 framework are preferably used toprovide the sequences required for expression of the cleaved DNA.

Preferably, the double-stranded portion of the adapter is about 12 to100 bases in length. More preferably, about 20 to 100 bases are used.The double-standard region of the adapter also preferably contains atleast one endonuclease recognition site useful for cloning the DNA intoa suitable display and/or expression vector (or a recipient vector usedto archive the diversity). This endonuclease restriction site may benative to the germline gene sequences used to extend the DNA sequence.It may be also constructed using degenerate sequences to the nativegermline gene sequences. Or, it may be wholly synthetic.

The single-stranded portion of the adapter is complementary to theregion of the cleavage in the single-stranded DNA. The overlap can befrom about 2 bases up to about 15 bases. The longer the overlap, themore efficient the ligation is likely to be. A preferred length for theoverlap is 7 to 10. This allows some mismatches in the region so thatdiversity in this region may be captured.

The single-stranded region or overlap of the partially duplexed adapteris advantageous because it allows DNA cleaved at the chosen site, butnot other fragments to be captured. Such fragments would contaminate thelibrary with genes encoding sequences that will not fold into properantibodies and are likely to be non-specifically sticky.

One illustration of the use of a partially duplexed adaptor in themethods of this invention involves ligating such adaptor to a human FR3region that has been cleaved, as described above, at 5′-ACnGT-3′ usingHpyCH4III, Bst4CI or TaaI.

Table 4 F.2 shows the bottom strand of the double-stranded portion ofthe adaptor for ligation to the cleaved bottom-strand DNA. Since theHpyCH4III-Site is so far to the right (as shown in Table 3), a sequencethat includes the AflI-site as well as the XbaI site can be added. Thisbottom strand portion of the partially-duplexed adaptor, H43.XAExt,incorporates both XbaI and AMl-sites. The top strand of thedouble-stranded portion of the adaptor has neither site (due to plannedmismatches in the segments opposite the XbaI and AfII-Sites ofH43.XAExt), but will anneal very tightly to H43.XAExt. H43AExt containsonly the AflII-site and is to be used with the top strands H43.ABr1 andH43.ABr2 (which have intentional alterations to destroy the AflII-site).

After ligation, the desired, captured DNA can be PCR amplified again, ifdesired, using in the preferred embodiment a primer to the downstreamconstant region of the antibody gene and a primer to part of thedouble-standard region of the adapter. The primers may also carryrestriction endonuclease sites for use in cloning the amplified DNA.

After ligation, and perhaps amplification, of the partiallydouble-stranded adapter to the single-stranded amplified DNA, thecomposite DNA is cleaved at chosen 5′ and 3′ endonuclease recognitionsites.

The cleavage sites useful for cloning depend on the phage or phagemid orother vectors into which the cassette will be inserted and the availablesites in the antibody genes. Table 19 provides restriction endonucleasedata for 75 human light chains. Table 20 shows corresponding data for 79human heavy chains. In each Table, the endonucleases are ordered byincreasing frequency of cutting. In these Tables, Nch is the number ofchains cut by the enzyme and Ns is the number of sites (some chains havemore than one site).

From this analysis, SfiI, NotI, AflII, ApaLI, and AscI are verysuitable. SfiI and NotI are preferably used in pCES1 to insert theheavy-chain display segment. ApaLI and AscI are preferably used in pCES1to insert the light-chain display segment.

BstEII-sites occur in 97% of germ-line JH genes. In rearranged V genes,only 54/79 (68%) of heavy-chain genes contain a BstEII-Site and 7/61 ofthese contain two sites. Thus, 47/79 (59%) contain a single BstEII-Site.An alternative to using BstEII is to cleave via UREs at the end of JHand ligate to a synthetic oligonucleotide that encodes part of CH1.

One example of preparing a family of DNA sequences using the methods ofthis invention involves capturing human CDR 3 diversity. As describedabove, mRNAs from various autoimmune patients are reverse transcribedinto lower strand cDNA. After the top strand RNA is degraded, the lowerstrand is immobilized and a short oligonucleotide used to cleave thecDNA upstream of CDR3. A partially duplexed synthetic DNA adapter isthen annealed to the DNA and the DNA is amplified using a primer to theadapter and a primer to the constant region (after FR4). The DNA is thencleaved using BstEII (in FR4) and a restriction endonuclease appropriateto the partially double-stranded adapter (e.g., XbaI and AflII (inFR3)). The DNA is then ligated into a synthetic VH skeleton such as3-23.

One example of preparing a single-stranded DNA that was cleaved usingthe URE method involves the human Kappa chain. The cleavage site in thesense strand of this chain is depicted in Table 17. The oligonucleotidekapextURE is annealed to the oligonucleotides (kaBRO1UR, kaBR02UR,kaBRO3UR, and kaBRO4UR) to form a partially duplex DNA. This DNA is thenligated to the cleaved soluble kappa chains. The ligation product isthen amplified using primers kapextUREPCR and CKForeAsc (which inserts aAscI site after the end of C kappa). This product is then cleaved withApaLI and AscI and ligated to similarly cut recipient vector.

Another example involves the cleavage of lambda light chains,illustrated in Table 18. After cleavage, an extender (ON_LamEx133) andfour bridge oligonucleotides (ON_LamB1-133, ON_LamB2-133, ON_LamB3-133,and ON_LamB4-133) are annealed to form a partially duplex DNA. That DNAis ligated to the cleaved lambda-chain sense strands. After ligation,the DNA is amplified with ON_Lam133PCR and a forward primer specific tothe lambda constant domain, such as CL2ForeAsc or CL7ForeAsc (Table130).

In human heavy chains, one can cleave almost all genes in FR4(downstream, i.e., toward the 3′ end of the sense strand, of CDR3) at aBstEII-Site that occurs at a constant position in a very large fractionof human heavy-chain V genes. One then needs a site in FR3, if only CDR3diversity is to be captured, in FR2, if CDR2 and CDR3 diversity iswanted, or in FR1, if all the CDR diversity is wanted. These sites arepreferably inserted as part of the partially double-stranded adaptor.

The preferred process of this invention is to provide recipient vectors(e.g., for display and/or expression) having sites that allow cloning ofeither light or heavy chains. Such vectors are well known and widelyused in the art. A preferred phage display vector in accordance withthis invention is phage MALIA3. This displays in gene III. The sequenceof the phage MALIA3 is shown in Table 21A (annotated) and Table 21B(condensed).

The DNA encoding the selected regions of the light or heavy chains canbe transferred to the vectors using endonucleases that cut either lightor heavy chains only very rarely. For example, light chains may becaptured with ApaLI and AscI. Heavy-chain genes are preferably clonedinto a recipient vector having SfiI, NcoI, XbaI, AflII, BstEII, ApaI,and NotI sites. The light chains are preferably moved into the libraryas ApaLI-AscI fragments. The heavy chains are preferably moved into thelibrary as SfiI-NotI fragments.

Most preferably, the display is had on the surface of a derivative ofM13 phage. The most preferred vector contains all the genes of M13, anantibiotic resistance gene, and the display cassette. The preferredvector is provided with restriction sites that allow introduction andexcision of members of the diverse family of genes, as cassettes. Thepreferred vector is stable against rearrangement under the growthconditions used to amplify phage.

In another embodiment of this invention, the diversity captured by themethods of the present invention may be displayed and/or expressed in aphagemid vector (e.g., pCES1) that displays and/or expresses thepeptide, polypeptide or protein. Such vectors may also be used to storethe diversity for subsequent display and/or expression using othervectors or phage.

In another embodiment of this invention, the diversity captured by themethods of the present invention may be displayed and/or expressed in ayeast vector.

In another embodiment, the mode of display may be through a short linkerto anchor domains—one possible anchor comprising the final portion ofM13 III (“IIIstump”) and a second possible anchor being the full lengthIII mature protein.

The IIIstump fragment contains enough of M13 III to assemble into phagebut not the domains involved in mediating infectivity. Because the w.t.III proteins are present the phage is unlikely to delete the antibodygenes and phage that do delete these segments receive only a very smallgrowth advantage. For each of the anchor domains, the DNA encodes thew.t. AA sequence, but differs from the w.t. DNA sequence to a very highextent. This will greatly reduce the potential for homologousrecombination between the anchor and the w.t. gene that is also present(see Example 6).

Most preferably, the present invention uses a complete phage carrying anantibiotic-resistance gene (such as an ampicillin-resistance gene) andthe display cassette. Because the w.t. iii and possibly viii genes arepresent, the w.t. proteins are also present. The display cassette istranscribed from a regulatable promoter (e.g., P_(LacZ)). Use of aregulatable promoter allows control of the ratio of the fusion displaygene to the corresponding w.t. coat protein. This ratio determines theaverage number of copies of the display fusion per phage (or phagemid)particle.

Another aspect of the invention is a method of displaying peptides,polypeptides or proteins (and particularly Fabs) on filamentous phage.In the most preferred embodiment this method displays FABs andcomprises:

-   a) obtaining a cassette capturing a diversity of segments of DNA    encoding the elements:-   P_(reg)::RBS1::SS1::VL::CL::stop::RBS2::SS2::VH::CH1::linker::anchor::stop::,    where P_(reg) is a regulatable promoter, RBS1 is a first ribosome    binding site, SS1 is a signal sequence operable in the host strain,    VL is a member of a diverse set of light-chain variable regions, CL    is a light-chain constant region, stop is one or more stop codons,    RBS2 is a second ribosome binding site, SS2 is a second signal    sequence operable in the host strain, VH is a member of a diverse    set of heavy-chain variable regions, CH1 is an antibody heavy-chain    first constant domain, linker is a sequence of amino acids of one to    about 50 residues, anchor is a protein that will assemble into the    filamentous phage particle and stop is a second example of one or    more stop codons; and-   b) positioning that cassette within the phage genome to maximize the    viability of the phage and to minimize the potential for deletion of    the cassette or parts thereof.

The DNA encoding the anchor protein in the above preferred cassetteshould be designed to encode the same (or a closely related) amino acidsequence as is found in one of the coat proteins of the phage, but witha distinct DNA sequence. This is to prevent unwanted homologousrecombination with the w.t. gene. In addition, the cassette should beplaced in the intergenic region. The positioning and orientation of thedisplay cassette can influence the behavior of the phage.

In one embodiment of the invention, a transcription terminator may beplaced after the second stop of the display cassette above (e.g., Trp).This will reduce interaction between the display cassette and othergenes in the phage antibody display vector.

In another embodiment of the methods of this invention, the phage orphagemid can display and/or express proteins other than Fab, byreplacing the Fab portions indicated above, with other protein genes.

Various hosts can be used the display and/or expression aspect of thisinvention. Such hosts are well known in the art. In the preferredembodiment, where Fabs are being displayed and/or expressed, thepreferred host should grow at 30° C. and be RecA⁻ (to reduce unwantedgenetic recombination) and EndA⁻ (to make recovery of RF DNA easier). Itis also preferred that the host strain be easily transformed byelectroporation.

XL1-Blue MRF′ satisfies most of these preferences, but does not growwell at 30° C. XL1-Blue MRF′ does gLow slowly at 38° C. and thus is anacceptable host. TG-1 is also an acceptable host although it is RecA′and EndA⁺. XL1-Blue MRF′ is more preferred for the intermediate hostused to accumulate diversity prior to final construction of the library.

After display and/or expression, the libraries of this invention may bescreened using well known and conventionally used techniques. Theselected peptides, polypeptides or proteins may then be used to treatdisease. Generally, the peptides, polypeptides or proteins for use intherapy or in pharmaceutical compositions are produced by isolating theDNA encoding the desired peptide, polypeptide or protein from the memberof the library selected. That DNA is then used in conventional methodsto produce the peptide, polypeptides or protein it encodes inappropriate host cells, preferably mammalian host cells, e.g., CHOcells. After isolation, the peptide, polypeptide or protein is usedalone or with pharmaceutically acceptable compositions in therapy totreat disease.

EXAMPLES Example 1: RACE Amplification of Heavy and Light Chain AntibodyRepertoires from Autoimmune Patients

Total RNA was isolated from individual blood samples (50 ml) of 11patients using a RNAzol™ kit (CINNA/Biotecx), as described by themanufacturer. The patients were diagnosed as follows:

-   1. SLE and phospholipid syndrome-   2. limited systemic sclerosis-   3. SLE and Sjogren syndrome-   4. Limited Systemic sclerosis-   5. Reumatoid Arthritis with active vasculitis-   6. Limited systemic sclerosis and Sjogren Syndrome-   7. Reumatoid Artritis and (not active) vasculitis-   8. SLE and Sjogren syndrome-   9. SLE-   10. SLE and (active) glomerulonephritis-   11. Polyarthritis/Raynauds Phenomen

From these 11 samples of total RNA, Poly-A+ RNA was isolated usingPromega PolyATtractO mRNA Isolation kit (Promega).

250 ng of each poly-A+ RNA sample was used to amplify antibody heavy andlight chains with the GeneRAacer™ kit (Invitrogen cat no. L1500-01). Aschematic overview of the RACE procedure is shown in FIG. 3.

Using the general protocol of the GeneRAacer™ kit, an RNA adaptor wasligated to the 5′end of all mRNAs. Next, a reverse transcriptasereaction was performed in the presence of oligo(dT15) specific primerunder conditions described by the manufacturer in the GeneRAacer™ kit.

1/5 of the cDNA from the reverse transcriptase reaction was used in a 20ul PCR reaction. For amplification of the heavy chain IgM repertoire, aforward primer based on the CH1 chain of IgM [HuCmFOR] and a backwardprimer based on the ligated synthetic adaptor sequence [5′A] were used.(See Table 22)

For amplification of the kappa and lambda light chains, a forward primerthat contains the 3′ coding-end of the cDNA [HuCkFor andHuCLFor2+HuCLfor7] and a backward primer based on the ligated syntheticadapter sequence [5′A] was used (See Table 22). Specific amplificationproducts after 30 cycles of primary PCR were obtained.

FIG. 4 shows the amplification products obtained after the primary PCRreaction from 4 different patient samples. 8 ul primary PCR product from4 different patients was analyzed on a agarose gel [labeled 1, 2, 3 and4]. For the heavy chain, a product of approximately 950 nt is obtainedwhile for the kappa and lambda light chains the product is approximately850 nt. M1-2 are molecular weight markers.

PCR products were also analyzed by DNA sequencing [10 clones from thelambda, kappa or heavy chain repertoires]. All sequenced antibody genesrecovered contained the full coding sequence as well as the 5′ leadersequence and the V gene diversity was the expected diversity (comparedto literature data).

50 ng of all samples from all 11 individual amplified samples were mixedfor heavy, lambda light or kappa light chains and used in secondary PCRreactions.

In all secondary PCRs approximately 1 ng template DNA from the primaryPCR mixture was used in multiple 50 ul PCR reactions [25 cycles].

For the heavy chain, a nested biotinylated forward primer [HuCm-Nested]was used, and a nested 5′end backward primer located in the syntheticadapter-sequence [5′NA] was used. The 5′end lower-strand of the heavychain was biotinylated.

For the light chains, a 5′end biotinylated nested primer in thesynthetic adapter was used [5′NA] in combination with a 3′end primer inthe constant region of Ckappa and Clambda, extended with a sequencecoding for the AscI restriction site [kappa: HuCkForAscI, Lambda:HuCL2-FOR-ASC+HuCL7-FOR-ASC]. [5′end Top strand DNA was biotinylated].After gel-analysis the secondary PCR products were pooled and purifiedwith Promega Wizzard PCR cleanup.

Approximately 25 ug biotinylated heavy chain, lambda and kappa lightchain DNA was isolated from the 11 patients.

Example 2: Capturing Kappa Chains with BamAI

A repertoire of human-kappa chain mRNAs was prepared using the RACEmethod of Example 1 from a collection of patients having variousautoimmune diseases.

This Example followed the protocol of Example 1. Approximately 2micrograms (ug) of human kappa-chain (Igkappa) gene RACE material withbiotin attached to 5′-end of upper strand was immobilized as in Example1 on 200 microliters (μL) of Seradyn magnetic beads. The lower strandwas removed by washing the DNA with 2 aliquots 200 μL of 0.1 M NaOH (pH13) for 3 minutes for the first aliquot followed by 30 seconds for thesecond aliquot. The beads were neutralized with 200 μL of 10 mM Tris (pH7.5) 100 mM NaCl. The short oligonucleotides shown in Table 23 wereadded in 40 fold molar excess in 100 μL of NEB buffer 2 (50 mM NaCl, 10mM Tris-HCl, 10 mM MgCl₂, 1 mM dithiothreitol pH 7.9) to the dry beads.The mixture was incubated at 95° C. for 5 minutes then cooled down to55° C. over 30 minutes. Excess oligonucleotide was washed away with 2washes of NEB buffer 3 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl₂, 1 mMdithiothreitol pH 7.9). Ten units of BsmAI (NEB) were added in NEBbuffer 3 and incubated for 1 h at 55° C. The cleaved downstream DNA wascollected and purified over a Qiagen PCR purification column (FIGS. 5and 6).

FIG. 5 shows an analysis of digested kappa single-stranded DNA.Approximately 151.5 pmol of adapter was annealed to 3.79 pmol ofimmobilized kappa single-stranded DNA followed by digestion with 15 U ofBsmAI. The supernatant containing the desired DNA was removed andanalyzed by 5% polyacrylamide gel along with the remaining beads whichcontained uncleaved full length kappa DNA. 189 pmol of cleavedsingle-stranded DNA was purified for further analysis. Five percent ofthe original full length ssDNA remained on the beads.

FIG. 6 shows an analysis of the extender-cleaved kappa ligation. 180pmol of pre-annealed bridge/extender was ligated to 1.8 pmol of BsmAIdigested single-stranded DNA. The ligated DNA was purified by Qiagen PCRpurification column and analyzed on a 5% polyacrylamide gel. Resultsindicated that the ligation of extender to single-stranded DNA was 95%efficient.

A partially double-stranded adaptor was prepared using theoligonucleotide shown in Table 23. The adaptor was added to thesingle-stranded DNA in 100 fold molar excess along with 1000 units of T4DNA ligase and incubated overnight at 16° C. The excess oligonucleotidewas removed with a Qiagen PCR purification column. The ligated materialwas amplified by PCR using the primers kapPCRt1 and kapfor shown inTable 23 for 10 cycles with the program shown in Table 24.

The soluble PCR product was run on a gel and showed a band ofapproximately 700 n, as expected (FIGS. 7 and 8). The DNA was cleavedwith enzymes ApaLI and AscI, gel purified, and ligated to similarlycleaved vector pCES1.

FIG. 7 shows an analysis of the PCR product from the extender-kappaamplification. Ligated extender-kappa single-stranded DNA was amplifiedwith primers specific to the extender and to the constant region of thelight chain. Two different template concentrations, 10 ng versus 50 ng,were used as template and 13 cycles were used to generate approximately1.5 ug of dsDNA as shown by 0.8% agarose gel analysis.

FIG. 8 shows an analysis of the purified PCR product from theextender-kappa amplification. Approximately 5 ug of PCR amplifiedextender-kappa double-stranded DNA was run out on a 0.8% agarose gel,cut out, and extracted with a GFX gel purification column. By gelanalysis, 3.5 ug of double-stranded DNA was prepared.

The assay for capturing kappa chains with BsmAl was repeated andproduced similar results. FIG. 9A shows the DNA after it was cleaved andcollected and purified over a Qiagen PCR purification column. FIG. 9Bshows the partially double-stranded adaptor ligated to thesingle-stranded DNA. This ligated material was then amplified (FIG. 9C).The gel showed a band of approximately 700 n.

Table 25 shows the DNA sequence of a kappa light chain captured by thisprocedure. Table 26 shows a second sequence captured by this procedure.The closest bridge sequence was complementary to the sequence5′-agccacc-3′, but the sequence captured reads 5′-Tgccacc-3′, showingthat some mismatch in the overlapped region is tolerated.

Example 3: Construction of Synthetic CDR1 and CDR2 Diversity in V-3-23VH Framework

Synthetic diversity in Complementary Determinant Region (CDR) 1 and 2was created in the 3-23 VH framework in a two step process: first, avector containing the 3-23 VH framework was constructed; and then, asynthetic CDR 1 and 2 was assembled and cloned into this vector.

For construction of the 3-23 VH framework, 8 oligonucleotides and twoPCR primers (long oligonucleotides—TOPFR1A, BOTFR1B, BOTFR2, BOTFR3,F06, BOTFR4, ON-vgC1, and ON-vgC2 and primers—SFPRMET and BOTPCRPRIM,shown in Table 27) that overlap were designed based on the Genebanksequence of 3-23 VH framework region. The design incorporated at leastone useful restriction site in each framework region, as shown in Table27. In Table 27, the segments that were synthesized are shown as bold,the overlapping regions are underscored, and the PCR priming regions ateach end are underscored.

A mixture of these 8 oligos was combined at a final concentration of 2.5uM in a 20 ul PCR reaction. The PCR mixture contained 200 uM dNTPs, 2.5mM MgCl₂, 0.02 U Pfu Turbo™ DNA Polymerase, 1 U Qiagen HotStart Taq DNAPolymerase, and 1× Qiagen PCR buffer. The PCR program consisted of 10cycles of 94_C for 30 s, 55_C for 30 s, and 72_C for 30 s.

The assembled 3-23 VH DNA sequence was then amplified, using 2.5 ul of a10-fold dilution from the initial PCR in 100 ul PCR reaction. The PCRreaction contained 200 uM dNTPs, 2.5 mM MgCl₂, 0.02 U Pfu Turbo™ DNAPolymerase, 1 U Qiagen HotStart Taq DNA Polymerase, 1× Qiagen PCR Bufferand 2 outside primers (SFPRMET and BOTPCRPRIM) at a concentration ofluM. The PCR program consisted of 23 cycles at 94_C for 30 s, 55_C for30 s, and 72_C for 60 s. The 3-23 VH DNA sequence was digested andcloned into pCES1 (phagemid vector) using the SfiI and BstEIIrestriction endonuclease sites. All restriction enzymes mentioned hereinwere supplied by New England BioLabs, Beverly, Mass. and used as per themanufacturer's instructions.

Stuffer sequences (shown in Table 28 and Table 29) were introduced intopCES1 to replace CDR1/CDR2 sequences (900 bases between BspEI and XbaIRE sites) and CDR3 sequences (358 bases between AflII and BstEII) priorto cloning the CDR1/CDR2 diversity. This new vector was termed pCES5 andits sequence is given in Table 29.

Having stuffers in place of the CDRs avoids the risk that a parentalsequence would be over-represented in the library. The stuffer sequencesare fragments from the penicillase gene of E. coli. The CDR1-2 stuffercontains restriction sites for BglII, Bsu36I, BclI, XcmI, MluI, PvuII,HpaI, and HincII, the underscored sites being unique within the vectorpCES5. The stuffer that replaces CDR3 contains the unique restrictionendonuclease site RsrII.

A schematic representation of the design for CDR1 and CDR2 syntheticdiversity is shown FIG. 10. The design was based on the presence ofmutations in DP47/3-23 and related germline genes. Diversity wasdesigned to be introduced at the positions within CDR1 and CDR2indicated by the numbers in FIG. 10. The diversity at each position waschosen to be one of the three following schemes: 1=ADEFGHIKLMNPQRSTVWY;2=YRWVGS; 3=PS, in which letters encode equimolar mixes of the indicatedamino acids.

For the construction of the CDR1 and CDR2 diversity, 4 overlappingoligonucleotides (ON-vgCl, ON_Br12, ON_CD2Xba, and ON-vgC2, shown inTable 27 and Table 30) encoding CDR1/2, plus flanking regions, weredesigned. A mixture of these 4 oligos was combined at a finalconcentration of 2.5 uM in a 40 ul PCR reaction. Two of the 4 oligoscontained variegated sequences positioned at the CDR1 and the CDR2. ThePCR mixture contained 200 uM dNTPs, 2.5 U Pwo DNA Polymerase (Roche),and 1× Pwo PCR buffer with 2 mM MgSO₄. The PCR program consisted of 10cycles at 94_C for 30 s, 60_C for 30 s, and 72_C for 60 s. Thisassembled CDR1/2 DNA sequence was amplified, using 2.5 ul of the mixturein 100 ul PCR reaction. The PCR reaction contained 200 uM dNTPs, 2.5 UPwo DNA Polymerase, 1× Pwo PCR Buffer with 2 mM MgSO₄ and 2 outsideprimers at a concentration of luM. The PCR program consisted of 10cycles at 94_C for 30 s, 60_C for 30 s, and 72_C for 60 s. Thesevariegated sequences were digested and cloned into the 3-23 VH frameworkin place of the CDR1/2 stuffer.

We obtained approximately 7×107 independent transformants. CDR3diversity either from donor populations or from synthetic DNA can becloned into the vector containing synthetic CDR1 and CDR 2 diversity.

A schematic representation of this procedure is shown in FIG. 11. Asequence encoding the FR-regions of the human V3-23 gene segment and CDRregions with synthetic diversity was made by oligonucleotide assemblyand cloning via BspE1 and Xba1 sites into a vector that complements theFR1 and FR3 regions. Into this library of synthetic VH segments, thecomplementary VH-CDR3 sequence (top right) was cloned via Xbal an BstEllsites. The resulting cloned CH genes contain a combination of designedsynthetic diversity and natural diversity (see FIG. 11).

Example 4: Cleavage and Ligation of the Lambda Light Chains with HinfI

A schematic of the cleavage and ligation of antibody light chains isshown in FIGS. 12A and 12B. Approximately 2 ug of biotinylated humanLambda DNA prepared as described in Example 1 was immobilized on 200 ulSeradyn magnetic beads. The lower strand was removed by incubation ofthe DNA with 200 ul of 0.1 M NaOH (pH=13) for 3 minutes, the supernatantwas removed and an additional washing of 30 seconds with 200 ul of 0.1 MNaOH was performed. Supernatant was removed and the beads wereneutralized with 200 ul of 10 mM Tris (pH=7.5), 100 mM NaCl. 2additional washes with 200 ul NEB2 buffer 2, containing 10 mM Tris(pH=7.9), 50 mM NaCl, 10 mM MgCl2 and 1 mM dithiothreitol, wereperformed. After immobilization, the amount of ssDNA was estimated on a5% PAGE-UREA gel.

About 0.8 ug ssDNA was recovered and incubated in 100 ul NEB2 buffer 2containing 80 molar fold excess of an equimolar mix of ON_Lam1aB7,ON_Lam2aB7, ON_Lam31B7 and ON_Lam3rB7 [each oligo in 20 fold molarexcess] (see Table 31).

The mixture was incubated at 95° C. for 5 minutes and then slowly cooleddown to 50° C. over a period of 30 minutes. Excess of oligonucleotidewas washed away with 2 washes of 200 ul of NEB buffer 2. 4 U/ug of HinfI was added and incubated for 1 hour at 50° C. Beads were mixed every 10minutes.

After incubation the sample was purified over a Qiagen PCR purificationcolumn and was subsequently analysed on a 5% PAGE-urea gel (see FIG.13A, cleavage was more than 70% efficient).

A schematic of the ligation of the cleaved liqht chains is shown in FIG.12B. A mix of bridge/extender pairs was prepared from the Brg/Extoligo's listed in Table 31 (total molar excess 100 fold) in 1000 U of T4DNA Ligase (NEB) and incubated overnight at 16° C. After ligation of theDNA, the excess oligonucleotide was removed with a Qiagen PCRpurification column and ligation was checked on a Urea-PAGE gel (seeFIG. 13B; ligation was more than 95% efficient).

Multiple PCRs were performed containing 10 ng of the ligated material inan 50 ul PCR reaction using 25 pMol ON lamPlePCR and 25 pmol of anequimolar mix of Hu-CL2AscI/HuCL7AscI primer (see Example 1). PCR wasperformed at 60° C. for 15 cycles using Pfu polymerase. About 1 ug ofdsDNA was recovered per PCR (see FIG. 13C) and cleaved with ApaL1 andAscI for cloning the lambda light chains in pCES2.

Example 5: Capture of Human Heavy-Chain CDR3 Population

A schematic of the cleavage and ligation of antibody light chains isshown in FIGS. 14A and 14B.

Approximately 3 ug of human heavy-chain (IgM) gene RACE material withbiotin attached to 5′-end of lower strand was immobilized on 300 uL ofSeradyn magnetic beads. The upper strand was removed by washing the DNAwith 2 aliquots 300 uL of 0.1 M NaOH (pH 13) for 3 minutes for the firstaliquot followed by 30 seconds for the second aliquot. The beads wereneutralized with 300 uL of 10 mM Tris (pH 7.5) 100 mM NaCl. TheREdaptors (oligonucleotides used to make single-stranded DNA locallydouble-stranded) shown in Table 32 were added in 30 fold molar excess in200 uL of NEB buffer 4 (50 mM Potasium Acetate, 20 mM Tris-Acetate, 10mM Magnesuim Acetate, 1 mM dithiothreitol pH 7.9) to the dry beads. TheREadaptors were incubated with the single-stranded DNA at 80° C. for 5minutes then cooled down to 55° C. over 30 minutes. Excess REdaptorswere washed away with 2 washes of NEB buffer 4. Fifteen units ofHpyCH4III (NEB) were added in NEB buffer 4 and incubated for 1 hour at55° C. The cleaved downstream DNA remaining on the beads was removedfrom the beads using a Qiagen Nucleotide removal column (see FIG. 15).

The Bridge/Extender pairs shown in Table 33 were added in 25 molarexcess along with 1200 units of T4 DNA ligase and incubated overnight at16° C. Excess Bridge/Extender was removed with a Qiagen PCR purificationcolumn. The ligated material was amplified by PCR using primersH43.XAExtPCR2 and Hucumnest shown in Table 34 for 10 cycles with theprogram shown in Table 35.

The soluble PCR product was run on a gel and showed a band ofapproximately 500 n, as expected (see FIG. 15B). The DNA was cleavedwith enzymes SfiI and NotI, gel purified, and ligated to similarlycleaved vector PCES1.

Example 6: Description of Phage Display Vector CJRA05, a Member of theLibrary Built in Vector DY3F7

Table 36 contains an annotated DNA sequence of a member of the library,CJRA05, see FIG. 16. Table 36 is to be read as follows: on each lineeverything that follows an exclamation mark “!” is a comment. Alloccurrences of A, C, G, and T before “!” are the DNA sequence. Case isused only to show that certain bases constitute special features, suchas restriction sites, ribosome binding sites, and the like, which arelabeled below the DNA. CJRA05 is a derivative of phage DY3F7, obtainedby cloning an ApaLI to NotI fragment into these sites in DY3F31. DY3F31is like DY3F7 except that the light chain and heavy chain genes havebeen replaced by “stuffer” DNA that does not code for any antibody.DY3F7 contains an antibody that binds streptavidin, but did not comefrom the present library.

The phage genes start with gene ii and continue with genes x, v, vii,ix, viii, iii, vi, i, and iv. Gene iii has been slightly modified inthat eight codons have been inserted between the signal sequence and themature protein and the final amino acids of the signal sequence havebeen altered. This allows restriction enzyme recognition sites EagI andXbaI to be present. Following gene iv is the phage origin of replication(ori). After on is bla which confers resistance to ampicillin (ApR). Thephage genes and bla are transcribed in the same sense.

After bla, is the Fab cassette (illustrated in FIG. 17) comprising:

-   -   a) PlacZ promoter,    -   b) A first Ribosome Binding Site (RBS1),    -   c) The signal sequence form M13 iii,    -   d) An ApaLI RERS,    -   e) A light chain (a kappa L20::JK1 shortened by one codon at the        V-J boundary in this case),    -   f) An AscI RERS,    -   g) A second Ribosome Binding Site (RBS2),    -   h) A signal sequence, preferably PelB, which contains,    -   i) An SfiI RERS,    -   j) A synthetic 3-23 V region with diversity in CDR1 and CDR2,    -   k) A captured CDR3,    -   l) A partially synthetic J region (FR4 after BstEII),    -   m) CH1,    -   n) A NotI RERS,    -   o) A His6 tag (SEQ ID NO: 12),    -   p) A cMyc tag,    -   q) An amber codon,    -   r) An anchor DNA that encodes the same amino-acid sequence as        codons 273 to 424 of M13 iii (as shown in Table 37).    -   s) Two stop codons,    -   t) An AvrII RERS, and    -   u) A trp terminator.

The anchor (item r) encodes the same amino-acid sequence as do codons273 to 424 of M13 iii but the DNA is approximately as different aspossible from the wild-type DNA sequence. In Table 36, the III′ stumpruns from base 8997 to base 9455. Below the DNA, as comments, are thedifferences with wild-type iii for the comparable codons with “!W.T” atthe ends of these lines. Note that Met and Trp have only a single codonand must be left as is. These AA types are rare. Ser codons can bechanged at all three base, while Leu and Arg codons can be changed attwo.

In most cases, one base change can be introduced per codon. This hasthree advantages: 1) recombination with the wild-type gene carriedelsewhere on the phage is less likely, 2) new restriction sites can beintroduced, facilitating construction; and 3) sequencing primers thatbind in only one of the two regions can be designed.

The fragment of M13 III shown in CJRA05 is the preferred length for theanchor segment. Alternative longer or shorter anchor segments defined byreference to whole mature III protein may also be utilized.

The sequence of M13 III consists of the following elements: SignalSequence::Domain 1 (D1)::Linker 1 (L1)::Domain 2 (D2)::Linker 2(L2)::Domain 3 (D3)::Transmembrane Segment (TM)::Intracellular anchor(IC) (see Table 38).

The pIII anchor (also known as trpIII) preferably consists ofD2::L2::D3::TM::IC. Another embodiment for the pIII anchor consists ofD2′::L2::D3::TM::IC (where D2′ comprises the last 21 residues of D2 withthe first 109 residues deleted). A further embodiment of the pIII anchorconsists of D2′(C>S)::L2::D3::TM::IC (where D2′(C>S) is D2′ with thesingle C converted to S), and d) D3::TM::IC.

Table 38 shows a gene fragment comprising the NotI site, His6 tag (SEQID NO: 12), cMyc tag, an amber codon, a recombinant enterokinasecleavage site, and the whole of mature M13 III protein. The DNA used toencode this sequence is intentionally very different from the DNA ofwild-type gene iii as shown by the lines denoted “W.T.” containing thew.t. bases where these differ from this gene. III is divided intodomains denoted “domain 1”, “linker 1”, “domain 2”, “linker 2”, “domain3”, “transmembrane segment”, and “intracellular anchor”.

Alternative preferred anchor segments (defined by reference to thesequence of Table 38) include:

codons 1-29 joined to codons 104-435, deleting domain 1 and retaininglinker 1 to the end;

codons 1-38 joined to codons 104-435, deleting domain land retaining therEK cleavage site plus linker 1 to the end from III;

codons 1-29 joined to codons 236-435, deleting domain 1, linker 1, andmost of domain 2 and retaining linker 2 to the end;

codons 1-38 joined to codons 236-435, deleting domain 1, linker 1, andmost of domain 2 and retaining linker ? to the end and the rEK cleavagesite;

codons 1-29 joined to codons 236-435 and changing codon 240 to Ser(e.g., agc), deleting domain 1, linker 1, and most of domain 2 andretaining linker 2 to the end; and codons 1-38 joined to codons 236-435and changing codon 240 to Ser (e.g., agc), deleting domain 1, linker 1,and most of domain 2 and retaining linker 2 to the end and the rEKcleavage site.

The constructs would most readily be made by methods similar to those ofWang and Wilkinson (Biotechniques 2001: 31(4)722-724) in which PCR isused to copy the vector except the part to be deleted and matchingrestriction sites are introduced or retained at either end of the partto be kept. Table 39 shows the oligonucleotides to be used in deletingparts of the III anchor segment. The DNA shown in Table 38 has an NheIsite before the DINDDRMA (residues 29-36 of SEQ ID NO: 594)_recombinantenterokinase cleavage site (rEKCS). If NheI is used in the deletionprocess with this DNA, the rEKCS site would be lost. This site could bequite useful in cleaving Fabs from the phage and might facilitatecapture of very high-affinity antibodies. One could mutagenize thissequence so that the NheI site would follow the rEKCS site, an Ala Seramino-acid sequence is already present. Alternatively, one could useSphI for the deletions. This would involve a slight change in amino acidsequence but would be of no consequence.

Example 7: Selection of Antigen Binders from an Enriched Library ofHuman Antibodies Using Phage Vector DY3F31

In this example the human antibody library used is described in de Haardet al., (Journal of Biological Chemistry, 274 (26): 18218-30 (1999).This library, consisting of a large non-immune human Fab phagemidlibrary, was first enriched on antigen, either on streptavidin or onphenyl-oxazolone (phOx). The methods for this are well known in the art.Two preselected Fab libraries, the first one selected once onimmobilized phOx-BSA (R1-ox) and the second one selected twice onstreptavidin (R2-strep), were chosen for recloning.

These enriched repertoires of phage antibodies, in which only a very lowpercentage have binding activity to the antigen used in selection, wereconfirmed by screening clones in an ELISA for antigen binding. Theselected Fab genes were transferred from the phagemid vector of thislibrary to the DY3F31 vector via ApaL1-Not1 restriction sites.

DNA from the DY3F31 phage vector was pretreated with ATP dependent DNAseto remove chromosomal DNA and then digested with ApaL1 and Not1. Anextra digestion with AscI was performed in between to preventself-ligation of the vector. The ApaL1/NotI Fab fragment from thepreselected libraries was subsequently ligated to the vector DNA andtransformed into competent XL1-blue MRF′ cells.

Libraries were made using vector:insert ratios of 1:2 for phOx-libraryand 1:3 for STREP library, and using 100 ng ligated DNA per 50 μl ofelectroporation-competent cells (electroporation conditions: one shockof 1700 V, 1 hour recovery of cells in rich SOC medium, plating onamplicillin-containing agar plates).

This transformation resulted in a library size of 1.6×10⁶ for R1-ox inDY3F31 and 2.1×10⁶ for R2-strep in DY3F31. Sixteen colonies from eachlibrary were screened for insert, and all showed the correct size insert(±1400 bp) (for both libraries).

Phage was prepared from these Fab libraries as follows. A representativesample of the library was inoculated in medium with ampicillin andglucose, and at OD 0.5, the medium exchanged for ampicillin and 1 mMIPTG. After overnight growth at 37° C., phage was harvested from thesupernatant by PEG-NaCl precipitation. Phage was used for selection onantigen. R1-ox was selected on phOx-BSA coated by passive adsorptiononto immunotubes and R2-strep on streptavidin coated paramagnetic beads(Dynal, Norway), in procedures described in de Haard et. al. and Markset. al., Journal of Molecular Biology, 222(3): 581-97 (1991). Phagetiters and enrichments are given in Table 40.

Clones from these selected libraries, dubbed R2-ox and R3-streprespectively, were screened for binding to their antigens in ELISA. 44clones from each selection were picked randomly and screened as phage orsoluble Fab for binding in ELISA. For the libraries in DY3F31, cloneswere first grown in 2TY-2% glucose-50 μg/ml AMP to an OD600 ofapproximately 0.5, and then grown overnight in 2TY-50 μg/ml AMP+/−1 mMIPTG. Induction with IPTG may result in the production of both phage-Faband soluble Fab. Therefore the (same) clones were also grown withoutIPTG. Table 41 shows the results of an ELISA screening of the resultingsupernatant, either for the detection of phage particles with antigenbinding (Anti-M13 HRP=anti-phage antibody), or for the detection ofhuman Fabs, be it on phage or as soluble fragments, either with usingthe anti-myc antibody 9E10 which detects the myc-tag that every Fabcarries at the C-terminal end of the heavy chain followed by aHRP-labeled rabbit-anti-Mouse serum (column 9E10/RAM-HRP), or withanti-light chain reagent followed by a HRP-labeled goat-anti-rabbitantiserum (anti-CK/CL Gar-HRP).

The results shows that in both cases antigen-binders are identified inthe library, with as Fabs on phage or with the anti-Fab reagents (Table41). IPTG induction yields an increase in the number of positives. Alsoit can be seen that for the phOx-clones, the phage ELISA yields morepositives than the soluble Fab ELISA, most likely due to the avidbinding of phage. Twenty four of the ELISA-positive clones were screenedusing PCR of the Fab-insert from the vector, followed by digestion withBstNI. This yielded 17 different patterns for the phOx-binding Fab's in23 samples that were correctly analyzed, and 6 out of 24 for thestreptavidin binding clones. Thus, the data from the selection andscreening from this pre-enriched non-immune Fab library show that theDY3F31 vector is suitable for display and selection of Fab fragments,and provides both soluble Fab and Fab on phage for screening experimentsafter selection.

Example 8: Selection of Phage-Antibody Libraries on StreptavidinMagnetic Beads

The following example describes a selection in which one first depletesa sample of the library of binders to streptavidin and optionally ofbinders to a non-target (i.e., a molecule other than the target that onedoes not want the selected Fab to bind). It is hypothesized that one hasa molecule, termed a “competitive ligand”, which binds the target andthat an antibody which binds at the same site would be especiallyuseful.

For this procedure Streptavidin Magnetic Beads (Dynal) were blocked oncewith blocking solution (2% Marvel Milk, PBS (pH 7.4), 0.01% Tween-20(“2% MPBST”)) for 60 minutes at room temperature and then washed fivetimes with 2% MPBST. 450 μL of beads were blocked for each depletion andsubsequent selection set.

Per selection, 6.25 μL of biotinylated depletion target (1 mg/mL stockin PBST) was added to 0.250 mL of washed, blocked beads (from step 1).The target was allowed to bind overnight, with tumbling, at 4° C. Thenext day, the beads are washed 5 times with PBST.

Per selection, 0.010 mL of biotinylated target antigen (1 mg/mL stock inPBST) was added to 0.100 mL of blocked and washed beads (from step 1).The antigen was allowed to bind overnight, with tumbling, at 4° C. Thenext day, the beads were washed 5 times with PBST.

In round 1, 2×10¹² up to 10¹³ plaque forming units (pfu) per selectionwere blocked against non-specific binding by adding to 0.500 mL of 2%MPBS (=2% MPBST without Tween) for 1 hr at RT (tumble). In later rounds,1011 pfu per selection were blocked as done in round 1.

Each phage pool was incubated with 50 μL of depletion target beads(final wash supernatant removed just before use) on a Labquake rotatorfor 10 min at room temperature. After incubation, the phage supernatantwas removed and incubated with another 50 μL of depletion target beads.This was repeated 3 more times using depletion target beads and twiceusing blocked streptavidin beads for a total of 7 rounds of depletion,so each phage pool required 350 μL of depletion beads.

A small sample of each depleted library pool was taken for titering.Each library pool was added to 0.100 mL of target beads (final washsupernatant was removed just before use) and allowed to incubate for 2hours at room temperature (tumble).

Beads were then washed as rapidly as possible (e.g., 3 minutes total)with 5×0.500 mL PBST and then 2× with PBS. Phage still bound to beadsafter the washing were eluted once with 0.250 mL of competitive ligand(˜1 μμM) in PBST for 1 hour at room temperature on a Labquake rotator.The eluate was removed, mixed with 0.500 mL Minimal A salts solution andsaved. For a second selection, 0.500 mL 100 mM TEA was used for elutionfor 10 min at RT, then neutralized in a mix of 0.250 mL of 1 M Tris, pH7.4+0.500 mL Min A salts.

After the first selection elution, the beads can be eluted again with0.300 mL of non-biotinylated target (1 mg/mL) for 1 hr at RT on aLabquake rotator. Eluted phage are added to 0.450 mL Minimal A salts.

Three eluates (competitor from 1st selection, target from 1st selectionand neutralized TEA elution from 2nd selection) were kept separate and asmall aliquot taken from each for titering. 0.500 mL Minimal A saltswere added to the remaining bead aliquots after competitor and targetelution and after TEA elution. Take a small aliquot from each was takenfor tittering.

Each elution and each set of eluted beads was mixed with 2×YT and analiquot (e.g., 1 mL with 1. E 10/mL) of XL1-Blue MRF′ E. coli cells (orother F′ cell line) which had been chilled on ice after having beengrown to mid-logarithmic phase, starved and concentrated (see procedurebelow—“Mid-Log prep of XL-1 blue MRF′ cells for infection”).

After approximately 30 minutes at room temperature, the phage/cellmixtures were spread onto Bio-Assay Dishes (243×243×18 mm, Nalge Nunc)containing 2XYT, 1 mM IPTG agar. The plates were incubated overnight at30° C. The next day, each amplified phage culture was harvested from itsrespective plate. The plate was flooded with 35 mL TBS or LB, and cellswere scraped from the plate. The resuspended cells were transferred to acentrifuge bottle. An additional 20 mL TBS or LB was used to remove anycells from the plate and pooled with the cells in the centrifuge bottle.The cells were centrifuged out, and phage in the supernatant wasrecovered by PEG precipitation. Over the next day, the amplified phagepreps were titered.

In the first round, two selections yielded five amplified eluates. Theseamplified eluates were panned for 2-3 more additional rounds ofselection using ˜1. E 12 input phage/round. For each additional round,the depletion and target beads were prepared the night before the roundwas initiated.

For the elution steps in subsequent rounds, all elutions up to theelution step from which the amplified elution came from were done, andthe previous elutions were treated as washes. For the bead infectionamplified phage, for example, the competitive ligand and target elutionswere done and then tossed as washes (see below). Then the beads wereused to infect E. coli. Two pools, therefore, yielded a total of 5 finalelutions at the end of the selection.

1st Selection Set

-   -   A. Ligand amplified elution: elute w/ ligand for 1 hr, keep as        elution    -   B. Target amplified elution w/ ligand for 1 hr, toss as wash        elute w/ target for 1 hr, keep as elution    -   C. Bead infect. amp. elution: elute w/ligand for 1 hr, toss as        wash elute w/ target for 1 hr, toss as wash elute w/ cell        infection, keep as elution

2nd Selection Let

-   -   A. TEA amplified elution; elute w/ TEA 10 min, keep as elution    -   B. Bead infect. amp. elution; elute w/ TEA 10 min, toss as wash        elute w/ cell infection, keep as elution

Mid-Log Prep of XL1 Blue MRF′ Cells for Infection

(based on Barbas et al. Phage Display manual procedure)

Culture XL1 blue MRF′ in NZCYM (12.5 mg/mL tet) at 37° C. and 250 rpmovernight. Started a 500 mL culture in 2 liter flask by diluting cells1/50 in NZCYM/tet (10 mL overnight culture added) and incubated at 37°C. at 250 rpm until OD600 of 0.45 (1.5-2 hrs) was reached. Shaking wasreduced to 100 rpm for 10 min. When OD600 reached between 0.55-0.65,cells were transferred to 2×250 mL centrifuge bottles, centrifuged at600 g for 15 min at 4° C. Supernatant was poured off. Residual liquidwas removed with a pipette.

The pellets were gently resuspended (not pipetting up and down) in theoriginal volume of 1×Minimal A salts at room temp. The resuspended cellswere transferred back into 2-liter flask, shaken at 100 rpm for 45 minat 37° C. This process was performed in order to starve the cells andrestore pili. The cells were transferred to 2×250 mL centrifuge bottles,and centrifuged as earlier.

The cells were gently resuspended in ice cold Minimal A salts (5 mL per500 mL original culture). The cells were put on ice for use ininfections as soon as possible.

The phage eluates were brought up to 7.5 mL with 2XYT medium and 2.5 mLof cells were added. Beads were brought up to 3 mL with 2XYT and 1 mL ofcells were added. Incubated at 37° C. for 30 min. The cells were platedon 2XYT, 1 mM IPTG agar large NUNC plates and incubated for 18 hr at 30°C.

Example 9: Incorporation of Synthetic Region in FR1/3 Region

Described below are examples for incorporating of fixed residues inantibody sequences for light chain kappa and lambda genes, and for heavychains. The experimental conditions and oligonucleotides used for theexamples below have been described in previous examples (e.g., Examples3 & 4).

The process for incorporating fixed FR1 residues in an antibody lambdasequence consists of 3 steps (see FIG. 18): (1) annealing ofsingle-stranded DNA material encoding VL genes to a partiallycomplementary oligonucleotide mix (indicated with Ext and Bridge), toanneal in this example to the region encoding residues 5-7 of the FR1 ofthe lambda genes (indicated with X . . . X; within the lambda genes theoverlap may sometimes not be perfect); (2) ligation of this complex; (3)PCR of the ligated material with the indicated primer (‘PCRpr’) and forexample one primer based within the VL gene. In this process the firstfew residues of all lambda genes will be encoded by the sequencespresent in the oligonucleotides (Ext., Bridge or PCRpr). After the PCR,the lambda genes can be cloned using the indicated restriction site forApaLI.

The process for incorporating fixed FR1 residues in an antibody kappasequence (FIG. 19) consists of 3 steps: (1) annealing of single-strandedDNA material encoding VK genes to a partially complementaryoligonucleotide mix (indicated with Ext and Bri), to anneal in thisexample to the region encoding residues 8-10 of the FR1 of the kappagenes (indicated with X . . . X; within the kappa genes the overlap maysometimes not be perfect); (2) ligation of this complex; (3) PCR of theligated material with the indicated primer (‘PCRpr’) and for example oneprimer based within the VK gene. In this process the first few (8)residues of all kappa genes will be encode by the sequences present inthe oligonucleotides (Ext., Bridge or PCRpr.). After the PCR, the kappagenes can be cloned using the indicated restriction site for ApaLI.

The process of incorporating fixed FR3 residues in a antibody heavychain sequence (FIG. 20) consists of 3 steps: (1) annealing ofsingle-stranded DNA material encoding part of the VH genes (for exampleencoding FR3, CDR3 and FR4 regions) to a partially complementaryoligonucleotide mix (indicated with Ext and Bridge), to anneal in thisexample to the region encoding residues 92-94 (within the FR3 region) ofVH genes (indicated with X . . . X; within the VH genes the overlap maysometimes not be perfect); (2) ligation of this complex; (3) PCR of theligated material with the indicated primer (‘PCRpr’) and for example oneprimer based within the VH gene (such as in the FR4 region). In thisprocess certain residues of all VH genes will be encoded by thesequences present in the oligonucleotides used here, in particular fromPCRpr (for residues 70-73), or from Ext/Bridge oligonucleotides(residues 74-91). After the PCR, the partial VH genes can be clonedusing the indicated restriction site for XbaI.

It will be understood that the foregoing is only illustrative of theprinciples of this invention and that various modifications can be madeby those skilled in the art without departing from the scope of andsprit of the invention.

TABLE 1 Human GLG FR3 sequences ! VH1 !66  67  68  69  70  71  72  73  74  75  76  77  78  79  80agg gtc acc atg acc agg gac acg tcc atc agc aca gcc tac atg !81  82  82a 82b 82c 83  84  85  86  87  88  89  90  91  92gag ctg agc agg ctg aga tct gac gac acg gcc gtg tat tac tgt ! 93  94  95gcg aga ga ! 1-02# 1 (SEQ ID NO: 34)aga gtc acc att acc agg gac aca tcc gcg agc aca gcc tac atggag ctg agc agc ctg aga tct gaa gac acg gct gtg tat tac tgtgcg aga ga ! 1-03# 2 (SEQ ID NO: 35)aga gtc acc atg acc agg aac acc tcc ata agc aca gcc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgcg aga gg ! 1-08# 3 (SEQ ID NO: 36)aga gtc acc atg acc aca gac aca tcc acg agc aca gcc tac atggag ctg agg agc ctg aga tct gac gac acg gcc gtg tat tac tgtgcg aga ga ! 1-18# 4 (SEQ ID NO: 37)aga gtc acc atg acc gag gac aca tct aca gac aca gcc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgca aca ga ! 1-24# 5 (SEQ ID NO: 38)aga gtc acc att acc agg gac agg tct atg agc aca gcc tac atggag ctg agc agc ctg aga tct gag gac aca gcc atg tat tac tgtgca aga ta ! 1-45# 6 (SEQ ID NO: 39)aga gtc acc atg acc agg gac acg tcc acg agc aca gtc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgcg aga ga ! 1-46# 7 (SEQ ID NO: 40)aga gtc acc att acc agg gac atg tcc aca agc aca gcc tac atggag ctg agc agc ctg aga tcc gag gac acg gcc gtg tat tac tgtgcg gca ga ! 1-58# 8 (SEQ ID NO: 41)aga gtc acg att acc gcg gac gaa tcc acg agc aca gcc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgcg aga ga ! 1-69# 9 (SEQ ID NO: 42)aga gtc acg att acc gcg gac aaa tcc acg agc aca gcc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgcg aga ga ! 1-e# 10 (SEQ ID NO: 43)aga gtc acc ata acc gcg gac acg tct aca gac aca gcc tac atggag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgtgca aca ga ! 1-f# 11 (SEQ ID NO: 44) ! VH2agg ctc acc atc acc aag gac acc tcc aaa aac cag gtg gtc cttaca atg acc aac atg gac cct gtg gac aca gcc aca tat tac tgtgca cac aga c! 2-05# 12 (SEQ ID NO: 45)agg ctc acc atc tcc aag gac acc tcc aaa agc cag gtg gtc cttacc atg acc aac atg gac cct gtg gac aca gcc aca tat tac tgtgca cgg ata c! 2-26# 13 (SEQ ID NO: 46)agg ctc acc atc tcc aag gac acc tcc aaa aac cag gtg gtc cttaca atg acc aac atg gac cct gtg gac aca gcc acg tat tac tgtgca cgg ata c! 2-70# 14 (SEQ ID NO: 47) ! VH3cga ttc acc atc tcc aga gac aac gcc aag aac tca ctg tat ctgcaa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgtgcg aga ga ! 3-07* 15 (SEQ ID NO: 48)cga ttc acc atc tcc aga gac aac gcc aag aac tcc ctg tat ctgcaa atg aac agt ctg aga gct gag gac acg gcc ttg tat tac tgtgca aaa gat e! 3-09#16 (SEQ ID NO: 49)cga ttc acc atc tcc agg gac aac gcc aag aac tca ctg tat ctgcaa atg aac agc ctg aga gcc gag gac acg gcc gtg tat tac tgtgcg aga ga ! 3-11# 17 (SEQ ID NO: 50)cga ttc acc atc tcc aga gaa aat gcc aag aac tcc ttg tat cttcaa atg aac agc ctg aga gcc ggg gac acg gct gtg tat tac tgtgca aga ga ! 3-13# 18 (SEQ ID NO: 51)aga ttc acc atc tca aga gat gat tca aaa aac acg ctg tat ctgcaa atg aac agc ctg aaa acc gag gac aca gcc gtg tat tac tgtacc aca ga ! 3-15# 19 (SEQ ID NO: 52)cga ttc acc atc tcc aga gac aac gcc aag aac tcc ctg tat ctgcaa atg aac agt ctg aga gcc gag gac acg gcc ttg tat cac tgtgcg aga ga ! 3-20# 20 (SEQ ID NO: 53)cga ttc acc atc tcc aga gac aac gcc aag aac tca ctg tat ctgcaa atg acc agc ctg aga gcc gag gac acg gct gtg tat tac tgtgcg aga ga ! 3-21# 21 (SEQ ID NO: 54)cgg ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctgcaa atg aac agc ctg aga gcc gag gac acg gcc gta tat tac tgtgcg aaa ga ! 3-23* 22 (SEQ ID NO: 55)cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctgcaa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgtgcg aaa ga ! 3 30# 23 (SEQ ID NO: 56)cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctgcaa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgtgcg aga ga ! 3303# 24 (SEQ ID NO: 57)cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctgcaa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgtgcg aaa ga ! 3305# 25 (SEQ ID NO: 58)cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctgcaa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgtgcg aga ga ! 3-33# 26 (SEQ ID NO: 59)cga ttc acc atc tcc aga gac aac agc aaa aac tcc ctg tat ctgcaa atg aac agt ctg aga act gag gac acc gcc ttg tat tac tgtgca aaa gat a! 3-43#27 (SEQ ID NO: 60)cga ttc acc atc tcc aga gac aat gcc aag aac tca ctg tat ctgcaa atg aac agc ctg aga gac gag gac acg gct gtg tat tac tgtgcg aga ga ! 3-48# 28 (SEQ ID NO: 61)aga ttc acc atc tca aga gat ggt tcc aaa agc atc gcc tat ctgcaa atg aac agc ctg aaa acc gag gac aca gcc gtg tat tac tgtact aga ga ! 3-49# 29 (SEQ ID NO: 62)cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat cttcaa atg aac agc ctg aga gcc gag gac acg gcc gtg tat tac tgtgcg aga ga ! 3-53# 30 (SEQ ID NO: 63)aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat cttcaa atg ggc agc ctg aga gct gag gac atg gct gtg tat tac tgtgcg aga ga ! 3-64# 31 (SEQ ID NO: 64)aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat cttcaa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgtgcg aga ga ! 3-66# 32 (SEQ ID NO: 65)aga ttc acc atc tca aga gat gat tca aag aac tca ctg tat ctgcaa atg aac agc ctg aaa acc gag gac acg gcc gtg tat tac tgtgct aga ga ! 3-72# 33 (SEQ ID NO: 66)agg ttc acc atc tcc aga gat gat tca aag aac acg gcg tat ctgcaa atg aac agc ctg aaa acc gag gac acg gcc gtg tat tac tgtact aga ca ! 3 73# 34 (SEQ ID NO: 67)cga ttc acc atc tcc aga gac aac gcc aag aac acg ctg tat ctgcaa atg aac agt ctg aga gcc gag gac acg gct gtg tat tac tgtgca aga ga ! 3-74# 35 (SEQ ID NO: 68)aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg cat cttcaa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgtaag aaa ga ! 3-d# 36 (SEQ ID NO: 69) ! VH4cga gtc acc ata tca gta gac aag tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gcg gac acg gcc gtg tat tac tgtgcg aga ga ! 4-04# 37 (SEQ ID NO: 70)cga gtc acc atg tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gtg gac acg gcc gtg tat tac tgtgcg aga aa ! 4-28# 38 (SEQ ID NO: 71)cga gtt acc ata tca gta aac acg tct aag aac cag ttc tcc ctgaag ctg agc tct gtg act gcc gcg gac acg gcc gtg tat tac tgtgcg aga ga ! 4301# 39 (SEQ ID NO: 72)cga gtc acc ata tca gta gac agg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gcg gac acg gcc gtg tat tac tgtgcc aga ga ! 4302# 40 (SEQ ID NO: 73)cga gtt acc ata tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg act gcc gca gac acg gcc gtg tat tac tgtgcc aga ga ! 4304# 41 (SEQ ID NO: 74)cga gtt acc ata tca gta gac acg tct aag aac cag ttc tcc ctgaag ctg agc tct gtg act gcc gcg gac acg gcc gtg tat tac tgtgcg aga ga ! 4-31# 42 (SEQ ID NO: 75)cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gcg gac acg gct gtg tat tac tgtgcg aga ga ! 4-34# 43 (SEQ ID NO: 76)cga gtc acc ata tcc gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gca gac acg gct gtg tat tac tgtgcg aga ca ! 4-39# 44 (SEQ ID NO: 77)cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gct gcg gac acg gcc gtg tat tac tgtgcg aga ga ! 4-59# 45 (SEQ ID NO: 78)cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gct gcg gac acg gcc gtg tat tac tgtgcg aga ga ! 4-61# 46 (SEQ ID NO: 79)cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctgaag ctg agc tct gtg acc gcc gca gac acg gcc gtg tat tac tgtgcg aga ga ! 4-b# 47 (SEQ ID NO: 80) ! VH5cag gtc acc atc tca gcc gac aag tcc atc agc acc gcc tac ctgcag tgg agc agc ctg aag gcc tcg gac acc gcc atg tat tac tgtgcg aga ca ! 5-51# 48 (SEQ ID NO: 81)cac gtc acc atc tca gct gac aag tcc atc agc act gcc tac ctgcag tgg agc agc ctg aag gcc tcg gac acc gcc atg tat tac tgtgcg aga ! 5-a# 49 (SEQ ID NO: 82) ! VH6cga ata acc atc aac cca gac aca tcc aag aac cag ttc tcc ctgcag ctg aac tct gtg act ccc gag gac acg gct gtg tat tac tgtgca aga ga ! 6-1# 50 (SEQ ID NO: 83) ! VH7cgg ttt gtc ttc tcc ttg gac acc tct gtc agc acg gca tat ctgcag atc tgc agc cta aag gct gag gac act gcc gtg tat tac tgtgcg aga ga ! 74.1# 51 (SEQ ID NO: 84)

TABLE 2 Enzymes that either cut 15 or more human GLGs orhave 5+-base recognition in FR3 Typical entry: REname Recognition #sitesGLGid#: base# GLGid#: base# GLGid#: base# . . .  BstEii Ggtnacc 2  1: 348: 3 There are 2 hits at base# 3 MaeIII gtnac 36  1: 4  2: 4  3: 4 4: 4  5: 4  6: 4  7: 4  8: 4  9: 4 10: 4 11: 4 37: 4 37: 58 38: 438: 58 39: 4 39: 58 40: 4 40: 58 41: 4 41: 58 42: 4 42: 53 43: 4 43: 5844: 4 44: 58 45: 4 45: 58 46: 4 46: 58 47: 4 47: 58 48: 4 49: 4 50: 58There are 24 hits at base# 4 Tsp45I atsac 33  1: 4  2: 4  3: 4  4: 4 5: 4  6: 4  7: 4  8: 4  9: 4 10: 4 11: 4 37: 4 37: 58 38: 4 38: 5839: 58 40: 4 40: 58 41: 58 42: 58 43: 4 43: 58 44: 4 44: 58 45: 4 45: 5846: 4 46: 58 47: 4 47: 58 48: 4 49: 4 50: 58There are 21 hits at base# 4 HpftI tcacc 45  1: 5  2: 5  3: 5  4: 5 5: 5  6: 5  7: 5  8: 5 11: 5 12: 5 12: 11 13: 5 14: 5 15: 5 16: 5 17: 518: 5 19: 5 20: 5 21: 5 22: 5 23: 5 24: 5 25: 5 26: 5 27: 5 28: 5 29: 530: 5 31: 5 32: 5 33: 5 34: 5 35: 5 36: 5 37: 5 33: 5 40: 5 43: 5 44: 545: 5 46: 5 47: 5 48: 5 49: 5 There are 44 hits at base# 5NlaIII CATG 26  1: 9  1: 42  2: 42  3: 9  3: 42  4: 9  4: 42  5: 9 5: 42  6: 42  6: 78  7: 9  7: 42  8: 21  8: 42  9: 42 10: 42 11: 4212: 57 13: 48 13: 57 14: 57 31: 72 38: 9 48: 78 49: 78There are 11 hits at base# 42 There are 1 hits at base# 48 Could causeraggedness. BsaJI Ccnngg 37  1: 14  2: 14  5: 14  6: 14  7: 14  8: 14 8: 65  9: 14 10: 14 11: 14 12: 14 13: 14 14: 14 15: 65 17: 14 17: 6518: 65 19: 65 20: 65 21: 65 22: 65 26: 65 29: 65 30: 65 33: 65 34: 6535: 65 37: 65 38: 65 39: 65 40: 65 42: 65 43: 65 48: 65 49: 65 50: 6551: 14 There are 23 hits at base# 65 There are 14 hits at base# 14AluI AGct 42  1: 47  2: 47  3: 47  4: 47  5: 47  6: 47  7: 47  8: 47 9: 47 10: 47 11: 47 16: 63 23: 63 24: 63 25: 63 31: 63 32: 63 36: 6337: 47 37: 52 38: 47 38: 52 39: 47 39: 52 40: 47 40: 52 41: 47 41: 5242: 47 42: 52 43: 47 43: 52 44: 47 44: 52 45: 47 45: 52 46: 47 46: 5247: 47 47: 52 49: 15 50: 47 There are 23 hits at base# 47There are 11 hits at base# 52 Only 5 bases from 47 BlpI GCtnagc 21 1: 48  2: 48  3: 48  5: 48  6: 48  7: 48  8: 48  9: 48 10: 48 11: 4837: 48 38: 48 39: 48 40: 48 41: 48 42: 48 43: 48 44: 48 45: 48 46: 4847: 48 There are 21 hits at base# 48 MwoI GCNNNNNnngc (SEQ ID NO: 85) 19 1: 48  2: 28 19: 36 22: 36 23: 36 24: 36 25: 36 26: 36 35: 36 37: 6739: 67 40: 67 41: 67 42: 67 43: 67 44: 67 45: 67 46: 67 47: 67There are 10 hits at base# 67 There are 7 hits at base# 36 DdeI Ctnag 7 1: 49  1: 58  2: 49  2: 58  3: 49  3: 58  3: 65  4: 49  4: 50  5: 49 5: 50  5: 65  6: 49  6: 58  6: 65  7: 49  7: 58  7: 65  8: 49  8: 58 9: 49  9: 58  9: 65 10: 49 10: 58 10: 65 11: 49 11: 58 11: 65 15: 5816: 58 16: 65 17: 58 18: 58 20: 58 21: 58 22: 58 23: 58 23: 65 24: 5824: 65 25: 58 25: 65 26: 58 27: 58 27: 65 28: 58 30: 58 31: 58 31: 6532: 58 32: 65 35: 58 36: 58 36: 65 37: 49 38: 49 39: 26 39: 49 40: 4941: 49 42: 26 42: 49 43: 49 44: 49 45: 49 46: 49 47: 49 48: 12 49: 1251: 65 There are 29 hits at base# 58There are 22 hits at base# 49 Only nine base from 58There are 16 hits at base# 65 Only seven bases from 58 BglII Agatct 11 1: 61  2: 61  3: 61  4: 61  5: 61  6: 61  7: 61  9: 61 10: 61 11: 6151: 47 There are 10 hits at base# 61 BstYI Rgatcy 12  1: 61  2: 61 3: 61  4: 61  5: 61  6: 61  7: 61  8: 61  9: 61 10: 61 11: 61 51: 47There are 11 hits at base# 61 Hpy188I TCNga 17  1: 64  2: 64  3: 64 4: 64  5: 64  6: 64  7: 64  8: 64  9: 64 10: 64 11: 64 16: 57 20: 5727: 57 35: 57 43: 67 49: 67 There are 11 hits at base# 64There are 4 hits at base# 57There are 2 hits at base# 67 Could be ragged.MslI CAYNNnnRTG (SEQ ID NO: 86) 44  1: 72  2: 72  3: 72  4: 72  5: 72 6: 72  7: 72  8: 72  9: 72 10: 72 11: 72 15: 72 17: 72 18: 72 19: 7221: 72 23: 72 24: 72 25: 72 26: 72 28: 72 29: 72 30: 72 31: 72 32: 7233: 72 34: 72 35: 72 36: 72 37: 72 38: 72 39: 72 40: 72 41: 72 42: 7243: 72 44: 72 45: 72 46: 72 47: 72 48: 72 49: 72 50: 72 51: 72There are 44 hits at base# 72 BsiEI CGRYcg 23  1: 74  3: 74  4: 74 5: 74  7: 74  8: 74  9: 74 10: 74 11: 74 17: 74 22: 74 30: 74 33: 7434: 74 37: 74 38: 74 39: 74 40: 74 41: 74 42: 74 45: 74 46: 74 47: 74There are 23 hits at base# 74 EaeI Yggccr 23  1: 74  3: 74  4: 74  5: 74 7: 74  8: 74  9: 74 10: 74 11: 74 17: 74 22: 74 30: 74 33: 74 34: 7437: 74 38: 74 39: 74 40: 74 41: 74 42: 74 45: 74 46: 74 47: 74There are 23 hits at base# 74 EagI Cggccg 23  1: 74  3: 74  4: 74  5: 74 7: 74  8: 74  9: 74 10: 74 11: 74 17: 74 22: 74 30: 74 33: 74 34: 7437: 74 38: 74 39: 74 40: 74 41: 74 42: 74 45: 74 46: 74 47: 74There are 23 hits at base# 74 HaeIII GGcc 97  1: 75  3: 75  4: 75  5: 75 7: 75  8: 75  9: 75 10: 75 11: 75 16: 75 17: 75 20: 75 22: 75 30: 7533: 75 34: 75 37: 75 38: 75 39: 75 40: 75 41: 75 42: 75 45: 75 46: 7547: 75 48: 63 49: 63 There are 25 hits at base# 75Bst4CI ACNgt 65° C. 63 Sites There is a third isoschismer  1: 86  2: 86 3: 86  4: 86  5: 86  6: 86  7: 34  7: 86  8: 86  9: 86 10: 86 11: 8612: 86 13: 86 14: 86 15: 36 15: 86 16: 53 16: 86 17: 36 17: 86 18: 8619: 86 20: 53 20: 86 21: 36 21: 86 22: 0 22: 86 23: 86 24: 86 25: 8626: 86 27: 53 27: 86 28: 36 28: 86 29: 86 30: 86 31: 86 32: 86 33: 3633: 86 34: 86 35: 53 35: 86 36: 86 37: 86 38: 86 39: 86 40: 86 41: 8642: 86 43: 86 44: 86 45: 86 46: 86 47: 86 48: 86 49: 86 50: 86 51: 051: 86 There are 51 hits at base# 86 All the other sites are well awayHpyCH4III ACNgt 63  1: 86  2: 86  3: 86  4: 86  5: 86  6: 86  7: 34 7: 86  8: 86  9: 86 10: 86 11: 86 12: 86 13: 86 14: 86 15: 36 15: 8616: 53 16: 86 17: 36 17: 86 18: 86 19: 86 20: 53 20: 86 21: 36 21: 8622: 0 22: 86 23: 86 24: 86 25: 86 26: 86 27: 53 27: 86 28: 36 28: 8629: 86 30: 86 31: 86 32: 86 33: 36 33: 86 34: 86 35: 53 35: 86 36: 8637: 86 38: 86 39: 86 40: 86 41: 86 42: 86 43: 86 44: 86 45: 86 46: 8647: 86 48: 86 49: 86 50: 86 51: 0 51: 86 There are 51 hits at base# 86HinfI Gantc 43  2: 2  3: 2  4: 2  5: 2  6: 2  7: 2  8: 2  9: 2  9: 2210: 2 11: 2 15: 2 16: 2 17: 2 18: 2 19: 2 19: 22 20: 2 21: 2 23: 2 24: 225: 2 26: 2 27: 2 28: 2 29: 2 30: 2 31: 2 32: 2 33: 2 33: 22 34: 2235: 2 36: 2 37: 2 38: 2 40: 2 43: 2 44: 2 45: 2 46: 2 47: 2 50: 60There are 38 hits at base# 2 MlyI GAGTCNNNNNn (SEQ ID NO: 87) 18  2: 2 3: 2  4: 2  5: 2  6: 2  7: 2  8: 2  9: 2 10: 2 11: 2 37: 2 38: 2 40: 243: 2 44: 2 45: 2 46: 2 47: 2 There are 18 hits at base# 2 PleI gagtc 18 2: 2  3: 2  4: 2  5: 2  6: 2  7: 2  8: 2  9: 2 10: 2 11: 2 37: 2 38: 240: 2 43: 2 44: 2 45: 2 46: 2 47: 2 There are 18 hits at base# 2AciI Ccgc 24  2: 26  9: 14 10: 14 11: 14 27: 74 37: 62 37: 65 33: 6239: 65 40: 62 40: 65 41: 65 42: 65 43: 62 43: 65 44: 62 44: 65 45: 6246: 62 47: 62 47: 65 48: 35 43: 74 49: 74 There are 8 hits at base# 62There are 8 hits at base# 65 There are 3 hits at basa# 14There are 3 hits at basa# 74 There are 1 hits at basa# 26There are 1 hits at base# 35 -″- Gcgg 11  8: 91  9: 16 10: 16 11: 1637: 67 39: 67 40: 67 42: 67 43: 67 45: 67 46: 67There are 7 hits at base# 67 There are 3 hits at base# 16There are 1 hits at base# 91 BsiHKAI GWGCWc 20  2: 30  4: 30  6: 30 7: 30  9: 30 10: 30 12: 89 13: 89 14: 89 37: 51 38: 51 39: 51 40: 5141: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51 Bsp1206I GDGCHc 20  2: 30  4: 30  6: 30 7: 30  9: 30 10: 30 12: 89 13: 89 14: 89 37: 51 38: 51 39: 51 40: 5141: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51 HgiAi GWGCWc 20  2: 30  4: 30  6: 30 7: 30  9: 30 10: 30 12: 89 13: 89 14: 89 37: 51 38: 51 39: 51 40: 5141: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51 BsoFI Gangc 26  2: 53  3: 53  5: 53  6: 53 7: 53  8: 53  8: 91  9: 53 10: 53 11: 53 31: 53 36: 36 37: 64 39: 6440: 64 41: 64 42: 64 43: 64 44: 64 45: 64 46: 64 47: 64 48: 53 49: 5350: 45 51: 53 There are 13 hits at base# 53There are 10 hits at base# 64 TseI Gcwgc 17  2: 53  3: 53  5: 53  6: 53 7: 53  8: 53  9: 53 10: 53 11: 53 31: 53 36: 36 45: 64 46: 64 48: 5349: 53 50: 45 51: 53 There are 13 hits at base# 53 MnlI gagg 34  3: 67 3: 95  4: 51  5: 16  5: 67  6: 67  7: 67  8: 67  9: 67 10: 67 11: 6715: 67 16: 67 17: 67 19: 67 20: 67 21: 67 22: 67 23: 67 24: 67 25: 6726: 67 27: 67 28: 67 29: 67 30: 67 31: 67 32: 67 33: 67 34: 67 35: 6736: 67 50: 67 51: 67 There are 31 hits at base# 67 HpyCH4V TGca 34 5: 90  6: 90 11: 90 12: 90 13: 90 14: 90 15: 44 16: 44 16: 90 17: 4418: 90 19: 44 20: 44 21: 44 22: 44 23: 44 24: 44 25: 44 26: 44 27: 4427: 90 28: 44 29: 44 33: 44 34: 44 35: 44 35: 90 36: 38 48: 44 49: 4450: 44 50: 90 51: 44 51: 52 There are 21 hits at base# 44There are 1 hits at base# 52 AccI GTmkac 13 5-base recognition  7: 3711: 24 37: 16 38: 16 39: 16 40: 16 41: 16 42: 16 43: 16 44: 16 45: 1646: 16 47: 16 There are 11 hits at base# 15SacII CCGCgg 8 6-base recognition  9: 14 10: 14 11: 14 37: 65 39: 6540: 65 42: 65 43: 65 There are 5 hits at base# 65There are 3 hits at base# 14 TfiI Gawtc 24  9: 22 15: 2 16: 2 17: 218: 2 19: 2 19: 22 20: 2 21: 2 23: 2 24: 2 25: 2 26: 2 27: 2 28: 2 29: 230: 2 31: 2 32: 2 33: 2 33: 22 34: 22 35: 2 35: 2There are 20 hits at base# 2 BsmAI Nnnnnngagac (SEQ ID NO: 88) 19 15: 1116: 11 20: 11 21: 11 22: 11 23: 11 24: 11 25: 11 26: 11 27: 11 28: 1128: 56 30: 11 31: 11 32: 11 35: 11 36: 11 44: 87 48: 87There are 16 hits at base# 11 BpmI ctccag 19 15: 12 16: 12 17: 12 18: 1220: 12 21: 12 22: 12 23: 12 24: 12 25: 12 26: 12 27: 12 28: 12 30: 1231: 12 32: 12 34: 12 35: 12 36: 12 There are 19 hits at base# 12XmnI GAANNnnttc (SEQ ID NO: 89) 12 37: 30 39: 30 39: 30 40: 30 41: 3042: 30 43: 30 44: 30 45: 30 46: 30 47: 30 50: 30There are 12 hits at base# 30 BsrI NCcagt 12 37: 32 33: 32 39: 32 40: 3241: 32 42: 32 43: 32 44: 32 45: 32 46: 32 47: 32 50: 32There are 12 hits at base# 32 BanII GRGCYc 11 37: 51 38: 51 39: 5140: 51 41: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51 Ecl136I GAGctc 11 37: 51 38: 51 39: 5140: 51 41: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51 SacI GAGCTc 11 37: 51 38: 51 39: 51 40: 5141: 51 42: 51 43: 51 44: 51 45: 51 46: 51 47: 51There are 11 hits at base# 51

TABLE 3 Synthetic 3-23 FR3 of human heavy chains showningpositions of possible cleavage sites! Sites engineered into the synthetic gene are shown in upper case DNA! with the RE name between vertical bars (as in | XbaI |).! RERSs frequently found in GLGs are shown below the synthetic sequence! with the name to the right (as in gtn ac = MaeIII(24), indicating that! 24 of the 51 GLGs contain the site). !!                                                       |---FR3---!                                                        89  90 (codon #in !                                                         R   Fsynthetic 3-23                                                        |cgc|ttc|  6! Allowed DNA                                           |cgn|tty|!                                                       |agr|!                                                         ga ntc =HinfI(38)!                                                         ga gtc =PieI(18)!                                                         ga wtc =TfiI(20)!                                                            gtn ac =MaeIII(24)!                                                            gts ac =Tsp45I(21)!                                                              tc acc =HphI(44) !!       --------FR3--------------------------------------------------!         91  92  93  94  95  96  97  98  99 100 101 102 103 104 105!         T   I   S   R   D   N   S   K   N   T  L   Y   L   Q   M(SEQ ID NO: 91)        |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg| 51!allowed|acn|ath|tcn|cgn|gay|aay|tcn|aar|aay|acn|ttr|tay|ttr|car|atg|(SEQ ID NO: 90)!               |agy|agr|       |agy|           |ctn|   |ctn|    !               |     ga|gac = BsmAI(16)                      ag ct =   AluI(23)!              c|tcc ag = BpmI(19)                             g ctn agc =BlpI(21) !               |       |              g aan nnn ttc = XmnI(12)!               | XbaI  |                                 tg ca = HpyCH4v(21)! !       ---FR3----------------------------------------------------->|!        106 107 108 109 110 111 112 113 114 115 116 117 118 119 120!         N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K        |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa| 96!allowed|aay|tcn|ttr|cgn|gcn|gar|gay|acn|gcn|gtn|tay|tay|tgy|gcn|aar|!           |agy|ctn|agr|             |      |!              |      |   cc nnq q = BsaJI(23)        ac ngt = Bst4CI(51)!              |     aga tct = BglII(10)     |        ac ngt = HpyCH4III(51)!              |     Rga tcY = BstYI(11)     |        ac ngt = TaaI(51)!              |      |            c ayn nnn rtc = MslI(44)!              |      |               cg ryc g = BsiEI(23)!              |      |               yg gcc r = EaeI(23)!              |      |               cg gcc g = EagI(23)!              |      |               |g gcc = HaeIII(25)!              |      |      gag g = MnlI(31)|!              |AflII |               | PstI |

TABLE 4 REdaptors, Extenders, and Bridges used for Cleavage andCapture of Human Heavy Chains in FR3A: HpyCH4V Probes of actual human BC genes (SEQ ID NOs: 92-100,respectively, in order of appearance)!HpyCH4V in FR3 of human HC, bases 35-56; only those with TGca siteTGca; 10, RE recognition: tgca of length 4 is expected at 10  1 6-1agttctccctgcagctgaactc  2 3-11, 3-07, 3-21, 3-72, 3-48cactgtatctgcaaatgaacag  3 3-09, 3-43, 3-20 ccctgtatctgcaaatgaacag  45-51 ccgcctacctgcagtggagcag  53-15, 3-30, 3-30.5, 3-30.3, 3-74, 3-23, 3-33 cgctgtatctgcaaatgaacag  67-4.1 cggcatatctgcagatctgcag  7 3-73 cggcgtatctgcaaatgaacag  8 5-actgcctacctgcagtggagcag  9 3-49 tcgoctatctqcaaatgaacagB: HpyCH4V REdaptors, Extenders, and Bridges B.1 REdaptors! Cutting HC lower strand:  ! TmKeller for 100 mM NaCl, zero formamide! Edapters for cleavage SEQ T_(m) ^(W) T_(m) ^(K) ID NO:  (ON_HCFR36-1)5′-agttctcccTGCAgctgaactc-3′ 68.0 64.5 92 (ON_HCFR36-1A5′-ttctcccTGCAgctgaactc-3 62.0 62.5 residues 3-22 of 92 (ON_HCFR36-1B)5′-ttctcccTGCAgctgaac-3′ 56.0 59.9 residues 3-20 of 92 (ON_HCFR33-15)5′-cgctgtatcTGCAaatgaacag-3′ 64.0 60.8 96 (ON_HCFR33-15A)5′-ctgtatcTGCAaatgaacaa-3′ 56.0 56.3 residues 3-22 of 96 (ON_HCFR33-15B)5′-ctgtatcTGCAaatgaac-3′ 50.0 53.1 residues 3-20 of 96 (ON_HCFR33-11)5′-cactgtatcTGCAaatgaacag-3′ 62.0 58.9 93 (ON_HCFR35-51)5′-ccgcctaccTGCAgtggagcag-3′ 74.0 70.1 95 !B.2 Segment of synthetic 3-23 gene into which captured CDR3 is tobe cloned !                   XbaI... (SEQ ID NO: 101)!D323* cgCttcacTaag tcT aga gac aaC tcT aag aaT acT ctC taC! scab... designed gene 3-23 gene... ! ! HpyCH4V!  .. ..            AflII... ! Ttg caG atg aac agc TtA agG . . .! ........................... . . . ! B.3 Extender and Bridges! Extender (bottom strand):  ! (SEQ ID NO: 102)(ON_HCHpyEx01) 5′-cAAgTAgAgAgTATTcTTAgAgTTgTcTcTAgAcTTAgTgAgcg-3′! ON_HCApyEx01 is the reverse complement of! 5′-cgCttcacTaag tcT aga gac aaC tcT aag aaT acT ctC tat Ttg -3′ !! Bridges (top strand, 9-base cverlao):  !(SEQ ID NO: 103)(ON_HCHpyBr016-1) 5′-cgCttcacTaag tcT aga gac aaC tcT aag-                aaT acT ctC taC Ttg CAgctgaac-3′ (3′-term C is blocked)! ! 3-15 at al. + 3-11 (SEQ ID NO: 104)(ON HCHpyBr023-15) 5′-cgCttcacTaag tcT aga gac aaC tcT aag-                 aaT acT ctC taC Ttg CAaatgaac-3′ (3′-term C isblocked)  ! ! 5-51 (SEQ ID NO: 105)(ON_HCHpyBr045-51) 5′-cgCttcacTaag tcT aga gac aaC tcT aag-                 aaT acT ctC taC Ttg CAgtggagc-3′ (3′-term C is blocked)! ! PCR primer (top strand) !(ON_HCHpyPCR) 5′-cgCttcacTaag tcT aga gac-3′ (SEQ ID NO: 106) !C: BlpI Probes from human HC GLGs 1 1-58, 1-03, 1-08, 1-69, 1-24, 1-45, 1-46, 1-f, 1-eacatggaGCTGAGCagcctgag (SEQ ID NO: 107)  2 1-02acatggaGCTGAGCaggctgag (SEQ ID NO: 108)  3 1-18acatggagctgaggagcctgag (SEQ ID NO: 109)  4 5-51, 5-aacctgcagtggagcagcctgaa (SEQ ID NO: 110)  5 3-15,3-73,3-49,3-72atctgcaaatgaacagcctgaa (SEQ ID NO: 111) 6 3303, 3-33, 3-01,3-11,3-30,3-21,3-23,3305,3-48atctgcaaatgaacagcctgag (SEQ ID NO: 112)  7 3-20,3-74,3-09,3-43atctgcaaatgaacagtctgag (SEQ ID NO: 113)  8 74.1atctgcagatctgcagcctaaa (SEQ ID NO: 114)  9 3-66,3-13,3-53,3-0atcttcaaatgaacagcctgag (SEQ ID NO: 115) 10 3-64atcttcaaatgggcagcctgag (SEQ ID NO: 116)11 4301,4-28,4302,4-04,4304,4-31,4-34,4-39,4-59,4-61,4-hccctgaaGCTGAGCtctgtgac (SEQ ID NO: 117) 12 6-1ccctgcagctgaactctgtgac (SEQ ID NO: 118) 13 2-70,2-05tccttacaatgaccaacatgga (SEQ ID NO: 119) 14 2-26tccttaccatgaccaacatgga (SEQ ID NO: 120)D: BlpI REdaptors, Extenders, and Bridges D.1 REdaptors T_(m) ^(W) T_(m)^(K) (BlpF3HC1-58) 5′-ac atg gaG CTG AGC agc ctg ag-3′ 70 66.4(SEQ ID NO: 12) (BlpF3HC6-1) 5′-cc ctg aag ctg agc tct gtg ac-3′ 70 66.4(SEQ ID NO: 122) ! BlpF3HC6-1 matches 4-30.1, not 6-1.D.2 Segment of synthetic 3-23 gene into which captured CDR3 is tobe cloned ! BlpI !                   XbaI... ... ...!D323* cgCttcacTaag TCT AGA gac aaC tcT aag aaT acT ctC taC TtgcaG atg aac (SEQ ID NO: 123) ! !                     AflII...!                   agC TTA AGG D.3 Extender and Bridges ! Bridges(BlpF3Br1) 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG-                  taC Ttg caG Ctg a|GC agc ctg-3′ (SEQ ID NO: 124)(BlpF3Br2) 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG-                  taC Ttg caG Ctg a|gc tct gtg-3′ (SEQ ID NO: 125)!                                  | lower strand is cut here ! Extender(BlpF3Ext) 5′-TcAgcTgcAAgTAcAAAgTATTTTTAcTgTTATcTcTAgAcTgAgTgAAgog-3′ (SEQ ID NO: 126) ! BlpF3Ext is the reverse complement of: ! 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG taC Ttg caGCtg a-3′ (SEQ ID NO: 127) !(BlpF3PCR) 5′-cgCttcacTcag tcT aga gaT aaC-3′E: HpyCH4III Distinct GLG sequences surrounding site, bases 77-98  1102#1, 118#4, 146#7, 169#9, 1e#10, 311#17, 353#30,404#37, 4301ccgtgtattactgtgcgagaga (SEQ ID NO: 128)  2103#2, 307#15, 321#21, 3303#24, 333#26, 348#28, 364#31, 366#32ctgtgtattactgtgcgagaga (SEQ ID NO: 129)  3108#3 ccgtgtattactgtgcgagagg (SEQ ID NO: 130)  4124#5, 1f#11 ccgtatattactgtgcaacaga (SEQ ID NO: 131)  5145#6 ccatgtattactgtgcaagata (SEQ ID NO: 132)  6158#8 ccgtgtattactgtgcggcaga (SEQ ID NO: 133)  7205#12 ccacatattactgtgcacacag (SEQ ID NO: 134)  8226#13 ccacatattactgtgcacggat (SEQ ID NO: 135)  9270#14 ccacgtattactgtgcacagat (SEQ ID NO: 136) 10309#16, 343#27 ccttgtattactgtgcaaaaga (SEQ ID NO: 137) 11313#18, 374#35, 61#50 ctgtgtattactgtgcaagaga (SEQ ID NO: 138) 12315#19 ccgtgtattactgtaccacaga (SEQ ID NO: 139) 13320#20 ccttgtatcactgtgcgagaga (SEQ ID NO: 140) 14323#22 ccgtatattactgtgcgaaaga (SEQ ID NO: 141) 15330#23, 3305#25 ctgtgtattactgtgcgaaaga (SEQ ID NO: 142) 16349#29 ccgtgtattactgtactagaga (SEQ ID NO: 143) 17372#33 ccgtgtattactgtgctagaga (SEQ ID NO: 144) 18373#34 ccgtgtattactgtactagaca (SEQ ID NO: 145) 193d#36 ctctgtattactgtaagaaaga (SEQ ID NO: 146) 20428#38 ccatgtattactgtgcgagaaa (SEQ ID NO: 147) 214302#40, 4304#41 ccgtgtattactgtgccagaga (SEQ ID NO: 148) 22439#44 ctgtgtattactgtgcgagaca (SEQ ID NO: 149) 23551#48 ccatgtattactgtgcgagaca (SEQ ID NO: 150) 245a#49 ccatgtattcctgtgcgaga (SEQ ID NO: 151)F: hpyCH4III REdaptors, Extenders, and Bridges F.1 REdaptors(SEQ ID NOs: 152 159, respectively, in order of appearance)! ONS for cleavaGe of HC(lower) in FR3(bases 77-97)! For cleavage with HpyCH4III, Bst4CI, or TaaI! cleavage id in lower chain before base 88. !   77 788 888 888 889 999 999 9 T_(m) ^(K)   78 901 234 567 890 123 456 7 T_(m) ^(W) (H43.77.97.1-02#1)5′-cc gtg tat tAC TGT gcg aga g-3′ 6462.6 (H43.77.97.1-03#2)5′-ct gtg tat tAC TGT gcg aga g-3′ 6260.6 (H43.77.97.108#3)5′-cc gtg tat tAC TGT gcg aga g-3′ 6462.6 (H43.77.97.323#22)5′-cc gta tat tac tgt gcg aaa g-3′ 6058.7 (H4377.97.330#23)5′-ct gtg tat tac tgt grg aaa g-3′ 6058.7 (H43.77.97.439#44)5′-ct gtg tat tac tgt gcg aga c-3′ 6260.6 (H43.77.97.551#48)5′-cc atg tat tac tgt gcg aga c-3′ 6760.6 (H43.77.97.5a#49)5′-cc atg tat tAC TGT gcg aga -3′ 5858.3 F.2 Extender and Bridges! XbaI and AflII sites in bridges are bunged (H43.XABr1) 5′-ggtgtagtga-|TCT|AGt|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- |aac|

aCT|GCA|Gtc|tac|tat tgt gcg aga-3′ (SEQ ID NO: 160)(H43.XABr2) 5′-ggtgtagtga-|TCT|AGt|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- |aac|

aCT|GCA|Gtc|tac|tat tgt gcg aaa-3′ (SEQ ID NO: 161)(H43.XAExt) 5′-ATAgTAgAcT gcAgTgTccT cAgcccTTAA gcTgTTcATc TgcAAgTAgA-gAgTATTcTT AgAgTTgTcT cTAgATcAcT AcAcc-3′(SEQ ID NO: 162)!H43.XAExt is the reverse complement of ! 5′-ggtgtagtga-! |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- ! |aac|

aCT|GCA|Gtc|tac|tat -3′ (SEQ ID NO:  638)(H43.XAPCR) 5′-ggtgtagtga |TCT|AGA|gac|aac-3′ (SEQ ID NO: 163)! XbaI and AflII sites in bridges are bunged (H43.ABr1) 5′-ggtgtagtga-|aac|

aCT|GCA|Gtc|tac|tat tgt gcg aga-3′ (SEQ ID NO: 164)(H43.ABr2) 5′-ggtgtagtga- |aac|

aCT|GCA|Gtc|tac|tat tgt gct aaa-3′ (SEQ ID NO: 165)(H43.AExt) 5′-ATAgTAgAcTgcAgTgTgTccTcAgcccTTAAgcTgTTTcAcTAcAcc-3′(SEQ ID NO: 166) !(H43.AExt) is the reverse complement of 5′-ggtgtagtga-! |aac|

aCT|GCA|Gtc|tac|tat -3′(SEQ ID NO:  167) (H43.APCR) 5′-ggtgtagtga |aac|

(SEQ ID NO: 168)

TABLE 5 Analysis of frequency of matching REdaptors in actual V genesA: HpyCH4V in HC at bases 35-56 Number of mismatches . . .  Number IdNtot 0 1 2 3 4 5 6 7 8 9 10 Cut Id Probe  1 510 5 11 274 92 61 25 22 111 3 5 443  6-1 agttctcccTGCAgctgaactc  2 192 54 42 32 24 15 2 3 10 3 1 6167  3-11 cactgtatcTGCAaatgaacag  3 58 19 7 17 6 5 1 0 1 0 2 0 54  3-09ccctgtatcTGCAaatgaacag  4 267 42 33 9 8 8 82 43 22 8 11 1 100  5-51ccgcctaccTGCAgtggagcag  5 250 111 59 41 24 7 5 1 0 0 2 0 242  3-15cgctgtatcTGCAaatgaacag  6 7 0 2 0 1 0 0 0 0 0 4 0 3  7-4.1cggcatatcTGCAgatctgcsg  7 7 0 2 2 0 0 2 1 0 0 0 0 4  3-73cggcgtatcTGCAastgaacag  8 26 10 4 1 3 1 2 1 3 1 0 0 19  5-actgcctaccTGCAgtggagcag  9 21 8 2 3 1 6 1 0 0 0 0 0 20  3-49tcgcctatcTGCAaatgaacsg 1338 249 162 379 149 103 120 71 47 13 23 12 1052(SEQ ID NO: 169-177, 249 411 790 939 1042 1162 1233 1280 1293 1316 1338respectively, in order of  appearance) Id Probe dotted probe  6-1agttctcccTGCAgctgaactc agttctcccTGCAgctgaactc  3-11cactgtatcTGCAaatgaacag cac.g.at.....aa.....ag  3-09ccctgtatcTGCAaatgaacag ccc.g.at.....aa.....ag  5-51ccgcctaccTGCAgtggagcag ccgc..a.......tg..g.ag  3-15cgctgtatcTGCAaatgaacag c.c.g.at.....aa.....ag  7-4.1cggcatatcTGCAgatctgcag c.gca.at......a.ctg.ag  3-73cggcgtatcTGCAaatgaacag c.gcg.at.....aa.....ag  5-actgcctaccTGCAgtggagcag ctgc..a.......tg..g.ag  3-49tcgcctatcTGCAaatgaacag tcgc..at.....aa.....ag(SEQ ID NO: 169-177, respectively, in order of appearance)Seqs with the expected RE site only . . . 1004(Counts only cases with 4 or fewer mismatches)Seqs with only an unexpected site . . . 0Seqs with both expected and unexpected . . . 48(Counts only cases with 4 or fewer mismatches)Seqs with no sites . . . 0 B: BlpI in HC Id Ntot 0 1 2 3 4 5 6 7 8 NcutName  1 133 73 16 11 13 6 9 1 4 0 119    1-58 acatggaGCTGAGCagcctgag  214 11 1 0 0 0 0 1 0 1 12    1-02 acatggagctgagcaggctgag  3 34 17 8 2 6 10 0 0 0 0    1-18 acatggagctgaggagcctgag  4 120 50 32 16 10 9 1 1 1 0 2   5-51 acctgcagtggagcagcctgaa  5 55 13 11 10 17 3 1 0 0 0 0    3-15atctgcaaatgaacagcctgaa  6 340 186 88 41 15 6 3 0 1 0 0 3303atctgcaaatgaacagcctgag  7 82 25 16 25 12 1 3 0 0 0 0    3-20atctgcaaatgaacagtctgag  8 3 0 2 0 1 0 0 0 0 0 0   74.1atctgcagatctgcagcctaaa  9 23 18 2 2 1 0 0 0 0 0 0    3-66atcttcaaatgaacagcctgag 10 2 1 0 1 0 0 0 0 0 0 0    3-64atcttcaaatgggcagcctgag 11 486 249 78 81 38 21 10 4 4 1 467 4301ccctgaagctgagctctgtgac 12 16 6 3 1 0 1 1 3 1 0 1    6-1ccctgcagctgaactctgtgac 13 28 15 6 2 2 1 0 0 0 0 0    2-70tccttacaatgaccaacatgga 14 2 0 2 0 0 0 0 0 0 0 0    2-26tccttaccatgaccaacatgga 601 (SEQ ID NO: 178-191,respectively in order of appearance) Name Full sequence Dot mode  1-58acatggaGCTGAGCagcctgag acatggaGCTGAGCagcctgag  1-02acatggagctgagcaagctgag ................g.....  1-18acatggagctgaggagcctgag .............g........  5-51acctgcagtggagcagcctgaa ..c..c..tg...........a  3-15atctgcaaatgaacagcctgaa .tc..c.aa...a........a  3-30.3atctgcaaatgaacagcctgag .tc..c.aa...a.........  3-20atctgcaaatgaacagtctgag .tc..c.aa...a...t.....  7-4.1atctgcagatctgcagcctaaa .tc..c..a.ct.......a.a  3-66atcttcaaatgaacagcctgag .tc.tc.aa...a.........  3-64atcttcaaatgggcagcctgag .tc.tc.aa..g..........  4-30.1ccctgaagctgagctctgtgac c.c..a........tctg...c  6-1ccctgcagctgaactctgtgac c.c..c......a.tctg...c  2-70tccttacaatgaccaacatgga t.c.tacaa...c..a.a..ga  2-26tccttaccatgaccaacatgga t.c.tacca...c..a.a..ga(SEQ ID NO: 178-191, respectively, in order of appearance)Seqs with the expected RE site only . . . 597 (counting sequences with 4 or fewer mismatches)Seqs with only an unexpected site . . . 2Seqs with both expected and unexpected . . . 2Seqs with no sites . . . 686 C: HpyCH4III, Bst4CI, or TaaI in HCIn scoring whether the RE site of interest is present, only ONs that have 4 or fewer mismatches are counted.Number of sequences . . . 1617 Id Ntot 0 1 2 3 4 5 6 7 8 Ncut acngtacngt  1 244 78 92 43 18 10 1 2 0 0 241 102#1,1 ccgtgtattACTGTgcgagagaccgtgtattactgtgcgagaga  2 457 69 150 115 66 34 11 8 3 1 434 103#2,3ctgtgtattactgtgcgagaga .t....................  3 173 52 45 36 22 14 3 00 1 169 108#3 ccgtgtattactgtgcgagagg .....................g  4 16 0 3 22 1 6 0 1 1 8 124#5,1 ccgtgtattactgtgcaacaga ................a.c...  5 40 0 1 0 1 1 0 1 0 2 145#6 ccatgtattactgtgcaagata ..a.............a...t. 6 15 1 0 1 0 6 4 1 1 1 3 15840 ccgtgtattactgtgcggcaga.................gc...  7 23 4 8 5 2 2 1 1 0 0 21 205#12ccacatattactgtgcacacag ..aca...........acacag  8 9 1 1 1 0 3 2 1 0 0 6226#13 ccacatattactgtgcacggat ..aca...........ac.gat  9 7 1 3 1 1 0 0 10 0 6 270#14 ccacgtattactgtgaacggat ..ac............ac.gat 10 23 7 3 5 52 1 0 0 0 22 309#16, ccttgtattactgtgcaaaaga ..t.............a.a... 11 355 10 7 6 3 3 0 2 0 31 313#18, ctgtgtattactgtgcaagaga.t..............a..... 12 18 2 3 2 2 6 1 0 2 0 15 315#19ccgtgtattactgtaccacaga ..............a.c.c... 13 3 1 2 0 0 0 0 0 0 0 3320#20 ccttgtatcactgtgcgagaga ..t.....c............. 14 117 29 23 28 228 4 2 1 0 110 323#22 ccgtatattactgtgcgaaaga ....a.............a... 15 7521 25 13 9 1 4 2 0 0 69 330#23, ctgtgtattactgtgcgaaaga.t................a... 16 14 2 2 2 3 0 3 1 1 0 9 349#29ccgtgtattactgtactagaga ..............a.t..... 17 2 0 0 1 0 0 1 0 0 0 1372#33 ccgtgtattactgtgctagaga ................t..... 18 1 0 0 1 0 0 0 00 0 1 373#34 ccgtgtattactgtactagaca ..............a.t...c. 19 2 0 0 0 00 0 0 0 2 0 3d#36 ctgtgtattactgtaagaaaga .t............aa..a... 20 34 49 9 4 5 3 0 0 0 31 428#38 ccgtgtattactgtgcgagaaa ....................a.21 17 5 4 2 2 3 1 0 0 0 16 4302#40 ccgtgtattactgtgccagaga................c..... 22 75 15 17 24 7 10 1 1 0 0 73 439#44ctgtgtattactgtgcgagaca .t..................c. 23 40 14 15 4 5 1 0 1 0 039 551#48 ccatgtattactgtgcgagaca ..a.................c. 24 213 26 56 6042 20 7 2 0 0 204 5a#49 ccatgtattactgtgcgagaAA ..a.................AAGroup 337 471 363 218 130 58 23 11 6 (SEQ ID NO: 192-215, Cumulative 337808 1171 1389 1519 1577 1600 1611 1617respectively, in order of appearanceSeqs with the expected RE site only 1511Seqs with only an unexpected site 0Seqs with both expected and unexpected 8 Seqs with no sites 0

TABLE 5D Analysis repeated using only 8 best REdaptorsId Ntot  0    1   2   3   4   5   6   7   8+1  301   78 101 54  32  16   9  10   1   0  281  102#1ccgtgtattactgtggagaga (SEQ ID NO: 267)2  493   69 155 125  73  37  14  11   3   6   459 103#2ctgtgtattactgtgcgagaga (SEQ ID NO: 263)3  189   52  45 38   23  13   5   4   1   3   176 108#3ccgtgtattactgtgcgagagg (SEQ ID NO: 269)4  127   29  23 28   24  10   6   5   2   0   114 323#22ccgtatattactgtgcgaaaga (SEQ ID NO: 270)5   78   21  25 14   11   1   4   2   0   0    72 330#23ctgtgtattactgtgcgaaaga (SEQ ID NO: 639)6   79   15  17  25   8   11   1   2   0   0    76 439#44ctgtgtattactgtgcgaaaca (SEQ ID NO: 272)7   43   14  15  5   5    3   0   1   0   0    42 551#48ccatgtattactgtgcgagaca (SEQ ID NO: 273)8  307   26  63  72  51  38  24  14  13   6   250 5a#49ccatgtattactgtgcgaaa (residues 1-20 of SEQ ID No: 274) 1 102#1ccgtgtattactgtgcgagaga ccgtgtattactgtgcgagaga 2 103#2ctgtgtattactgtqcgagaga .t.................... 3 108#3ccgtgtattactgtgcgagagg .....................g 4 323#22ccgtatattactgtgcgaaaga ...a..............a... 5 330#23ctgtgtattactgtgcgaaaga .t................a... 6 439#44ctgtgtattactgtqcqagaca .t..................c. 551#48ccatgtattactgtgcgagaca ..a.................c. 8 5a#49ccatatattactgtgcgagaAA ..a.................AA(SEQ ID NOs: 267-274, respectively, in order of appearance)Seqs with the expected RE site only  . . . 1463 / 1617Seqs with only an unexpected site . . .    0Seqs with both expected and unexpected . . .    7Seqs with no sites . . .    0

TABLE 6 Human HC GLG FR1 SequencesVH Exon - Nucleotide sequence alignment VH1 1-02CAG GTG CAG CTG GTG CAG TCT GGG GCT GAG GTG AAG AAG CCT GGG GCC TCA GTG AAG GTCTCC TGC AAG GCT TCT GGA TAC ACC TTC ACC (SEQ ID NO: 215) 1-03cag gtC cag ctT gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtTtcc tgc aag gct tct gga tac acc ttc acT (SEQ ID NO: 217) 1-08cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtctcc tgc aag gct tct gga tac acc ttc acc (SEQ ID NO: 218) 1-18cag gtT cag ctg gtg cag tct ggA gct gag gtg aag aag cct ggg gcc tca gtg aag gtctcc tgc aag gct tct ggT tac acc ttT acc (SEQ ID NO: 219) 1-24cag gtC cag ctg gtA cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtctcc tgc aag gTt tcC gga tac acc Ctc acT (SEQ ID NO: 220) 1-45cag Atg cag ctg gtg cag tct ggg gct gag gtg aag aag Act ggg Tcc tca gtg aag gtTtcc tgc aag gct tcC gga tac acc ttc acc (SEQ ID NO: 221) 1-46cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtTtcc tgc aag gcA tct gga tac acc ttc acc (SEQ ID NO: 222) 1-58caA Atg cag ctg gtg cag tct ggg Cct gag gtg aag aag cct ggg Acc tca gtg aag gtctcc tgc aag gct tct gga tTc acc ttT acT (SEQ ID NO: 223) 1-69cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg Tcc tcG gtg aag gtctcc tgc aag gct tct gga GGc acc ttc aGc (SEQ ID NO: 224) 1-ecag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg Tcc tcG gtg aag gtctcc tgc aag gct tct gga GGc acc ttc aGc (SEQ ID NO: 225) 1-fGag gtC cag ctg gtA cag tct ggg gct gag gtg aag aag cct ggg gcT Aca gtg aaA Atctcc tgc aag gTt tct gga tac acc ttc acc (SEQ ID NO: 225) VH2 2-05CAG ATC ACC TTG AAG GAG TCT GGT CCT ACG GTG GTG AAA CCC ACA CAG ACC CTC ACG CTGACC TGC ACC TTC TCT GGG TTC TCA CTC AGC (SEQ ID NO: 227) 2-25cag Gtc acc ttg aag gag tct ggt cct GTg ctg gtg aaa ccc aca Gag acc ctc acg ctgacc tgc acc Gtc tct ggg ttc tca ctc agc (SEQ ID NO: 228) 2-70cag Gtc acc ttg aag gag tct ggt cct Gcg ctg gtg aaa ccc aca cag acc ctc acA ctgacc tgc acc ttc tct ggg ttc tca ctc agc (SEQ ID NO: 229) VH3 3-07GAG GTG CAG CTG GTG GAG TCT GGG GGA GGC TTG GTC CAG CCT GGG GGG TCC CTG AGA CTCTCC TGT GCA GCC TCT GGA TTC ACC TTT AGT (SEQ ID NO: 230) 3-09gaA gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggC Agg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttt Gat (SEQ ID NO: 231) 3-11Cag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc Aag cct ggA ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 232) 3-13gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 233) 3-15gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA Aag cct ggg gag tcc ctT aga ctctcc tgt gca gcc tct gga ttc acT ttC agt (SEQ ID NO: 234) 3-20gag ttg cat ctg gtg gag tct ggg gga ggT Gtg gtA cGG cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttt Gat (SEQ ID NO: 235) 3-21gag gtg cag ctg gtg gag tct ggg gga ggc Ctg gtc Aag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc aca ttC agt (SEQ ID NO: 236) 3-23gag gtg cag ctg Ttg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttt agC (SEQ ID NO: 237) 3-30Cag gtg cag ctg gtg tag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 238) 3-30.3Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctctcc tgt gca gcc tct gga ttc aca ttC agt (SEQ ID NO: 239) 3-30.5Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 240) 3-33Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctctcc tgt gca gcG tct gga ttc acc ttC agt (SEQ ID NO: 241) 3-43gaA gtg cag ctg gtg gag tct ggg gga gTc Gtg gtA cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttt Gat (SEQ ID NO: 242) 3-48gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 243) 3-49gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag ccA ggg Cgg tcc ctg aga ctctcc tgt Aca gcT tct gga ttc act ttt Ggt (SEQ ID NO: 244) 3-53gag gtg cag ctg gtg gag Act ggA gga ggc ttg Atc cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct ggG ttc acc GtC agt (SEQ ID NO: 245) 3-64gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 246) 3-66gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc GtC agt (SEQ ID NO: 247) 3-72gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggA ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 248) 3-73gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aAa ctctcc tgt gca gcc tct ggG ttc acc ttC agt (SEQ ID NO: 249) 3-74gag gtg cag ctg gtg gag tcC ggg gga ggc ttA gtT cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc ttC agt (SEQ ID NO: 250) 3-dgag gtg cag ctg gtg gag tct Cgg gga gTc ttg gtA cag cct ggg ggg tcc ctg aga ctctcc tgt gca gcc tct gga ttc acc GtC agt (SEQ ID NO: 251) VH4 4-04CAG GTG CAG CTG CAG GAG TCG GGC CCA GGA CTG GTG AAG CCT TCG GGG ACC CTG TCC CTCACC TGC GCT GTC TCT GGT GGC TCC ATC AGC (SEQ ID NO: 252) 4-28cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAC acc ctg tcc ctcaac tgc gct gtc tct ggt TAc tcc atc agc (SEQ ID NO: 253) 4-30.1cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA CAg acc ctg tcc ctcacc tgc Act gtc tct ggt ggc tcc atc agc (SEQ ID NO: 254) 4-30.2cag Ctg cag ctg cag gag tcC ggc Tca gga ctg gtg aag cct tcA CAg acc ctg tcc ctcacc tgc gct gtc tct ggt ggc tcc atc agc (SEQ ID NO: 255) 4-30.4cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA CAg acc ctg tcc ctcacc tgc Act gtc tct ggt ggc tcc atc agc (SEQ ID NO: 256) 4-31cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA CAg acc ctg tcc ctcacc tgc Act gtc tct ggt ggc tcc atc agc (SEQ ID NO: 257) 4-34cag gtg cag ctA cag Cag tGg ggc Gca gga ctg Ttg aag cct tcg gAg acc ctg tcc ctcacc tgc gct gtc tAt ggt ggG tcc Ttc agT (SEQ ID NO: 258) 4-39cag Ctg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctcacc tgc Act gtc tct ggt atc tcc atc agc (SEQ ID NO: 259) 4-59cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctcacc tgc Act gtc tct ggt ggc tcc atc agT (SEQ ID NO: 260) 4-61cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctcacc tgc Act gtc tct ggt ggc tcc Gtc agc (SEQ ID NO: 261) 4-bcag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctcacc tgc gct gtc tct ggt TAc tcc atc agc (SEQ ID NO: 262) VH5 5-51GAG GTG CAG CTG GTG CAG TCT GGA GCA GAG GTG AAA AAG CCC GGG GAG TCT CTG AAG ATCTCC TGT AAG GGT TCT GGA TAC AGC TTT ACC (SEQ ID NO: 263) 5-agaA gtg cag ctg gtg cag tct gga gca gag gtg aaa aag ccc ggg gag tct ctg aGg atctcc tgt aag ggt tct gga tac agc ttt acc (SEQ ID NO: 264) VP6 6-1CAG GTA CAG CTG CAG CAG TCA GGT CCA GGA CTG GTG AAG CCC TCG CAG ACC CTC TCA CTCACC TGT GCC ATC TCC GGG GAC AGT GTC TCT (SEQ ID NO: 265) VH7 7-4.1CAG GTG CAG CTG GTG CAA TCT GGG TCT GAG TTG AAG AAG CCT GGG GCC TCA GTG AAG GTTTCC TGC AAG GCT TCT GGA TAC ACC TTC ACT (SEQ ID NO: 266)

TABLE 7 RERS sites in Human HC GLG FR1s where there are at least 20 GLGscut BsgI GTGCAG 71 (cuts 16/14 bases to right) 1: 4 1: 13 2: 13 3: 4 3:13 4: 13 6: 13 7: 4 7: 13 8: 13 9: 4 9: 13 10: 4 10: 13 15: 4 15: 65 16:4 16: 65 17: 4 17: 65 18: 4 18: 65 19: 4 19: 65 20: 4 20: 65 21: 4 21:65 22: 4 22: 65 23: 4 23: 65 24: 4 24: 65 25: 4 25: 65 26: 4 26: 65 27:4 27: 65 28: 4 28: 65 29: 4 30: 4 30: 65 31: 4 31: 65 32: 4 32: 65 33: 433: 65 34: 4 34: 65 35: 4 35: 65 36: 4 36: 65 37: 4 38: 4 39: 4 41: 442: 4 43: 4 45: 4 46: 4 47: 4 48: 4 48: 13 49: 4 49: 13 51: 4 There are39 hits at base# 4 There are 21 hits at base# 65 -″- ctqcac 9 12: 63 13:63 14: 63 39: 63 41: 63 42: 63 44: 63 45: 63 46: 63 BbvI GCAGC 65 1: 63: 6 6: 6 7: 6 8: 6 9: 6 10: 6 15: 6 15: 67 16: 6 16: 67 17: 6 17: 6718: 6 18: 67 19: 6 19: 67 20: 6 20: 67 21: 6 21: 67 22: 6 22: 67 23: 623: 67 24: 6 24: 67 25: 6 25: 67 26: 6 26: 67 27: 6 27: 67 28: 6 28: 6729: 6 30: 6 30: 67 31: 6 31: 67 32: 6 32: 67 33: 6 33: 67 34: 6 34: 6735: 6 35: 67 36: 6 36: 67 37: 6 38: 6 39: 6 40: 6 41: 6 42: 6 43: 6 44:6 45: 6 46: 6 47: 6 48: 6 49: 6 50: 12 51: 6 There are 43 hits at base#6 Bolded sites very near sites listed below There are 21 hits at base#67 -″- gctgc 13 37: 9 38: 9 39: 9 40: 3 40: 9 41: 9 42: 9 44: 3 44: 945: 9 46: 9 47: 9 50: 9 There are 11 hits at base # 9 BsoFI GCngc 78 1:6 3: 6 6: 6 7: 6 8: 6 9: 6 10: 6 15: 6 15: 67 16: 6 16: 67 17: 6 17: 6718: 6 18: 67 19: 6 19: 67 20: 6 20: 67 21: 6 21: 67 22: 6 22: 67 23: 623: 67 24: 6 24: 67 25: 6 25: 67 26: 6 26: 67 27: 6 27: 67 28: 6 28: 6729: 6 30: 6 30: 67 31: 6 31: 67 32: 6 32: 67 33: 6 33: 67 34: 6 34: 6735: 6 35: 67 36: 6 36: 67 37: 6 37: 9 38: 6 38: 9 39: 6 39: 9 40: 340: 6 40: 9 41: 6 41: 9 42: 6 42: 9 43: 6 44: 3 44: 6 44: 9 45: 6 45: 946: 6 46: 9 47: 6 47: 9 48: 6 49: 6 50: 9 50: 12 51: 6 There are 43 hitsat base# 6 These often occur together. There are 11 hits at base# 9There are 2 hits at base# 3 There are 21 hits at base# 67 TseI Gcwgc 781: 6 3: 6 6: 6 7: 6 8: 6 9: 6 10: 6 15: 6 15: 67 16: 6 16: 67 17: 6 17:67 18: 6 18: 67 19: 6 19: 67 20: 6 20: 67 21: 6 21: 67 22: 6 22: 67 23:6 23: 67 24: 6 24: 67 25: 6 25: 67 26: 6 26: 67 27: 6 27: 67 28: 6 28:67 29: 6 30: 6 30: 67 31: 6 31: 67 32: 6 32: 67 33: 6 33: 67 34: 6 34:67 35: 6 35: 67 36: 6 36: 67 37: 6 37: 9 38: 6 38: 9 39: 6 39: 9 40: 340: 6 40: 9 41: 6 41: 9 42: 6 42: 9 43: 6 44: 3 44: 6 44: 9 45: 6 45: 946: 6 46: 9 47: 6 47: 9 48: 6 49: 6 50: 9 50: 12 51: 6 There are 43 hitsat base# 6 Often together. There are 11 hits at base# 9 There are 2 hitsat base# 3 There are 1 hits at base# 12 There are 21 hits at base# 67MspA1I CMGckg 48 1: 7 3: 7 4: 7 5: 7 6: 7 7: 7 8: 7 9: 7 10: 7 11: 7 15:7 16: 7 17: 7 18: 7 19: 7 20: 7 21: 7 22: 7 23: 7 24: 7 25: 7 26: 7 27:7 28: 7 29: 7 30: 7 31: 7 32: 7 33: 7 34: 7 35: 7 36: 7 37: 7 38: 7 39:7 40: 1 40: 7 41: 7 42: 7 44: 1 44: 7 45: 7 46: 7 47: 7 48: 7 49: 7 50:7 51: 7 There are 46 hits at base# 7 PvuII CAGctg 48 1: 7 3: 7 4: 7 5: 76: 7 7: 7 8: 7 9: 7 10: 7 11: 7 15: 7 16: 7 17: 7 18: 7 19: 7 20: 7 21:7 22: 7 23: 7 24: 7 25: 7 26: 7 27: 7 28: 7 29: 7 30: 7 31: 7 32: 7 33:7 34: 7 35: 7 36: 7 37: 7 38: 7 39: 7 40: 1 40: 7 41: 7 42: 7 44: 144: 7 45: 7 46: 7 47: 7 48: 7 49: 7 50: 7 51: 7 There are 46 hits atbase# 7 There are 2 hits at base# 1 AluI AGct 54 1: 8 2: 8 3: 8 4: 8 4:24 5: 8 6: 8 7: 8 8: 8 9: 8 10: 8 11: 8 15: 8 16: 8 17: 8 18: 8 19: 820: 8 21: 8 22: 8 23: 8 24: 8 25: 8 26: 8 27: 8 28: 8 29: 8 29: 69 30: 831: 8 32: 8 33: 8 34: 8 35: 8 36: 8 37: 8 38: 8 39: 8 40: 2 40: 8 41: 842: 8 43: 8 44: 2 44: 8 45: 8 46: 8 47: 8 48: 8 48: 82 49: 8 49: 82 50:8 51: 8 There are 48 hits at base# 8 There are 2 hits at base# 2 DdeICtnag 48 1: 26 1: 48 2: 26 2: 48 3: 26 3: 48 4: 26 4: 48 5: 26 5: 48 6:26 6: 48 7: 26 7: 48 8: 26 8: 48 9: 26 10: 26 11: 26 12: 85 13: 85 14:85 15: 52 16: 52 17: 52 18: 52 19: 52 20: 52 21: 52 22: 52 23: 52 24: 5225: 52 26: 52 27: 52 28: 52 29: 52 30: 52 31: 52 32: 52 33: 52 35: 3035: 52 36: 52 40: 24 49: 52 51: 26 51: 48 There are 22 hits at base# 5252 and 48 never together. There are 9 hits at base# 48 There are 12 hitsat base# 26 26 and 24 never together. HphI tcacc 42 1: 86 3: 86 6: 86 7:86 8: 80 11: 86 12: 5 13: 5 14: 5 15: 80 16: 80 17: 80 18: 80 20: 80 21:80 22: 80 23: 80 24: 80 25: 80 26: 80 27: 80 28: 80 29: 80 30: 80 31: 8032: 80 33: 80 34: 80 35: 80 36: 80 37: 59 38: 59 39: 59 40: 59 41: 5942: 59 43: 59 44: 59 45: 59 46: 59 47: 59 50: 59 There are 22 hits atbase# 80 80 and 86 never together There are 5 hits at base# 86 There are12 hits at base# 59 BssKI Nccngg 50 1: 39 2: 39 3: 39 4: 39 5: 39 7: 398: 39 9: 39 10: 39 11: 39 15: 39 16: 39 17: 39 18: 39 19: 39 20: 39 21:29 21: 39 22: 39 23: 39 24: 39 25: 39 25: 39 27: 39 28: 39 29: 39 30: 3931: 39 32: 39 33: 39 34: 39 35: 19 35: 39 36: 39 37: 24 38: 24 39: 2441: 24 42: 24 44: 24 45: 24 46: 24 47: 24 48: 39 48: 40 49: 39 49: 4050: 24 50: 73 51: 39 There are 35 hits at base# 39 39 and 40 togethertwice. There are 2 hits at base# 40 BsaJI Ccnngg 47 1: 40 2: 40 3: 40 4:40 5: 40 7: 40 8: 40 9: 40 9: 47 10: 40 10: 47 11: 40 15: 40 18: 40 19:40 20: 40 21: 40 22: 40 23: 40 24: 40 25: 40 26: 40 27: 40 28: 40 29: 4030: 40 31: 40 32: 40 34: 40 35: 20 35: 40 36: 40 37: 24 38: 24 39: 2441: 24 42: 24 44: 24 45: 24 46: 24 47: 24 40: 40 48: 41 49: 40 49: 4150: 74 51: 40 There are 32 hits at base# 40 40 and 41 together twiceThere are 2 hits at base# 41 There are 9 hits at base# 24 There are 2hits at base# 47 BstNI CCwgg 44 PspGI ccwgg ScrFI ($M.HpaII) CCwgg CCwqg1: 40 2: 40 3: 40 4: 40 5: 40 7: 40 8: 40 9: 40 10: 40 11: 40 15: 40 16:40 17: 40 18: 40 19: 40 20: 40 21: 30 21: 40 22: 40 23: 40 24: 40 25: 4026: 40 27: 40 28: 40 29: 40 30: 40 31: 40 32: 40 33: 40 34: 40 35: 4036: 40 37: 25 36: 25 39: 25 41: 25 42: 25 44: 25 45: 25 46: 25 47: 2550: 25 51: 40 There are 33 hits at base# 40 ScrFi CCngg 50 1: 40 2: 403: 40 4: 40 5: 40 7: 40 8: 40 9: 40 10: 40 11: 40 15: 40 16: 40 17: 4018: 40 19: 40 20: 40 21: 30 21: 40 22: 40 23: 40 24: 40 25: 40 25: 4027: 40 28: 40 29: 40 30: 40 31: 40 32: 40 33: 40 34: 40 35: 20 35: 4036: 40 37: 25 38: 25 39: 25 41: 25 42: 25 44: 25 45: 25 46: 25 47: 2548: 40 43: 41 49: 40 49: 41 50: 25 50: 74 51: 40 There are 35 hits atbase# 40 There are 2 hits at base# 41 EcoO109I RGgnccy 34 1: 43 2: 43 3:43 4: 43 5: 43 6: 43 7: 43 8: 43 9: 43 10: 43 15: 46 16: 46 17: 46 18:46 19: 46 20: 46 21: 46 22: 46 23: 46 24: 46 25: 46 26: 46 27: 46 28: 4630: 46 31: 46 32: 46 33: 46 34: 46 35: 46 36: 46 37: 46 43: 79 51: 43There are 22 hits at base# 46 46 and 43 never together There are 11 hitsat base# 43 NlaTIV GGNncc 71 1: 43 2: 43 3: 43 4: 43 5: 43 6: 43 7: 438: 43 9: 43 9: 79 10: 43 10: 79 15: 46 15: 47 16: 47 17: 46 17: 4718: 46 18: 47 19: 46 19: 47 20: 46 20: 47 21: 46 21: 47 22: 46 22: 4723: 47 24: 47 25: 47 26: 47 27: 46 27: 47 28: 46 28: 47 29: 47 30: 4630: 47 31: 46 31: 47 32: 46 32: 47 33: 46 33: 47 34: 46 34: 47 35: 4635: 47 36: 46 36: 47 37: 21 37: 46 37: 47 37: 79 38: 21 39: 21 39: 7940: 79 41: 21 41: 79 42: 21 42: 79 43: 79 44: 21 44: 79 45: 21 45: 7946: 21 46: 79 47: 21 51: 43 There are 23 hits at base# 47 46 & 47 oftentogether There are 17 hits at base# 46 There are 11 hits at base# 43Sau96I Ggncc 70 1: 44 2: 3 2: 44 3: 44 4: 44 5: 3 5: 44 6: 44 7: 44 8:22 8: 44 9: 44 10: 44 11: 3 12: 22 13: 22 14: 22 15: 33 15: 47 16: 4717: 47 18: 47 19: 47 20: 47 21: 47 22: 47 23: 33 23: 47 24: 33 24: 4725: 33 25: 47 26: 33 26: 47 27: 47 28: 47 29: 47 30: 47 31: 33 31: 4732: 33 32: 47 33: 33 33: 47 34: 33 34: 47 35: 47 36: 47 37: 21 37: 2237: 47 38: 21 38: 22 39: 21 39: 22 41: 21 41: 22 42: 21 42: 22 43: 8044: 21 44: 22 45: 21 45: 22 46: 21 46: 22 47: 21 47: 22 50: 22 51: 44There are 23 hits at base# 47 These do not occur together. There are 11hits at base # 44 There are 14 hits at base# 22 These do occur together.There are 9 hits at base# 21 (SEQ ID NO: 13) BsmAI GTCTCNnnnn 22 1: 583: 58 4: 58 5: 58 8: 58 9: 58 10: 58 13: 70 36: 18 37: 70 38: 70 39: 7040: 70 41: 70 42: 70 44: 70 45: 70 46: 70 47: 70 48: 48 49: 48 50: 85There are 11 hits at base# 70 (SEQ ID NO: 14) -″- Nnnnnngagac 27 13: 4015: 48 16: 48 17: 48 18: 48 20: 48 21: 48 22: 48 23: 48 24: 48 25: 4826: 48 27: 48 28: 48 29: 48 30: 10 30: 48 31: 48 32: 48 33: 48 35: 4836: 48 43: 40 44: 40 45: 40 46: 40 47: 40 There are 20 hits at base# 48AvaII Gqwcc 44 Sau96I ($M.HaeIII) Ggwcc 44 2: 3 5: 3 6: 44 0: 44 9: 4410: 44 11: 3 12: 22 13: 22 14: 22 15: 33 15: 47 16: 47 17: 47 18: 47 19:47 20: 47 21: 47 22: 47 23: 33 23: 47 24: 33 24: 47 25: 33 25: 47 25: 3326: 47 27: 47 28: 47 29: 47 30: 47 31: 33 31: 47 32: 33 32: 47 33: 3333: 47 34: 33 34: 47 35: 47 36: 47 37: 47 43: 80 50: 22 There are 23hits at base# 47 44 & 47 never together There are 4 hits at base# 44PpuMI RGgwccy 27 6: 43 8: 43 9: 43 10: 43 15: 46 15: 46 17: 46 18: 4619: 46 20: 46 21: 46 22: 46 23: 46 24: 46 25: 46 26: 46 27: 46 28: 4630: 46 31: 46 32: 46 33: 46 34: 46 35: 46 36: 46 37: 46 43: 79 There are22 hits at base# 46 43 and 46 never occur together. There are 4 hits atbase# 43 BsmFI GGGAC 3 8: 43 37: 46 50: 77 -″- gtccc 33 15: 48 16: 4817: 48 1: 0 1: 0 20: 48 21: 48 22: 48 23: 48 24: 48 25: 48 26: 48 27: 4828: 48 29: 48 30: 48 31: 48 32: 48 33: 48 34: 48 35: 48 36: 48 37: 5438: 54 39: 54 40: 54 41: 54 42: 54 43: 54 44: 54 45: 54 46: 54 47: 54There are 20 hits at base# 48 There are 11 hits at base# 54 HinfI Gantc80 8: 77 12: 16 13: 16 14: 16 15: 16 15: 56 15: 77 16: 16 16: 56 16: 7717: 16 17: 56 17: 77 18: 16 18: 56 18: 77 19: 16 19: 56 19: 77 20: 1620: 56 20: 77 21: 16 21: 56 21: 77 22: 16 22: 56 22: 77 23: 16 23: 5623: 77 24: 16 24: 56 24: 77 25: 16 25: 56 25: 77 26: 16 26: 56 26: 7727: 16 27: 26 27: 56 27: 77 28: 16 28: 56 28: 77 29: 16 29: 56 29: 7730: 56 31: 16 31: 56 31: 77 32: 16 32: 56 32: 77 33: 16 33: 56 33: 7734: 16 35: 16 35: 56 35: 77 36: 16 36: 26 36: 56 36: 77 37: 16 38: 1639: 16 40: 16 41: 16 42: 16 44: 16 45: 16 46: 16 47: 16 48: 46 49: 46There are 34 hits at base# 16 TfiI Gawtc 21 8: 77 15: 77 16: 77 17: 7718: 77 19: 77 20: 77 21: 77 22: 77 23: 77 24: 77 25: 77 26: 77 27: 7728: 77 29: 77 31: 77 32: 77 33: 77 35: 77 36: 77 There are 21 hits atbase# 77 MlyI GAGTC 38 12: 16 13: 16 14: 16 15: 16 16: 16 17: 16 18: 1619: 16 20: 16 21: 16 22: 16 23: 16 24: 16 25: 16 26: 16 27: 16 27: 2628: 16 29: 16 31: 16 32: 16 33: 16 34: 16 35: 16 36: 16 36: 26 37: 1638: 16 39: 16 40: 16 41: 16 42: 16 44: 16 45: 16 46: 16 47: 16 48: 4649: 46 There are 34 hits at base# 16 -″- GACTC 21 15: 56 16: 56 17: 5618: 56 19: 56 20: 56 21: 56 22: 56 23: 56 24: 56 25: 56 26: 56 27: 5628: 56 29: 56 30: 56 31: 56 32: 56 33: 56 35: 56 36: 56 There are 21hits at base# 56 PleI gagtc 38 12: 16 13: 16 14: 16 15: 16 16: 16 17: 1618: 16 19: 16 20: 16 21: 16 22: 16 23: 16 24: 16 25: 16 26: 16 27: 1627: 26 28: 16 29: 16 31: 16 32: 16 33: 16 34: 16 35: 16 36: 16 36: 2637: 16 38: 16 39: 16 40: 16 41: 16 42: 16 44: 16 45: 16 46: 16 47: 1648: 46 49: 46 There are 34 hits at base# 16 -″- gactc 21 15: 56 16: 5617: 56 18: 56 19: 56 20: 56 21: 56 22: 56 23: 56 24: 56 25: 56 26: 5627: 56 28: 56 29: 56 30: 56 31: 56 32: 56 33: 56 35: 56 36: 56 There are21 hits at base# 56 AlwNI CAGNNNctg 26 15: 68 16: 68 17: 68 18: 68 19:68 20: 68 21: 68 22: 68 23: 68 24: 68 25: 68 26: 68 27: 68 28: 68 29: 6830: 68 31: 68 32: 68 33: 68 34: 68 35: 68 36: 68 39: 46 40: 46 41: 4642: 46 There are 22 hits at base# 68

TABLE 8 Kappa FR1 GLGs  ! 1   2   3   4   5   6   7   8   9   10  11  12O12 (SEQ ID NO: 275) GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT  !13  14  15  16  17  18  19  20  21  22  23GCA TCT CTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT O2 (SEQ ID NO: 276)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT O18 (SEQ ID NO: 277)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT O8 (SEQ ID NO: 278)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT A20 (SEQ ID NO: 279)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT A30 (SEQ ID NO: 280)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !AAC ATC CAG ATG ACC CAG TCT CCA TCT GCC ATG TCT L14 (SEQ ID NO: 281)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCA CTG TCT L1 (SEQ ID NO: 282)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !GAC ATC CAG ATG ACC CAG TCT CCA TCC TCA CTG TCT L15 (SEQ ID NO: 283)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !GCC ATC CAG TTG ACC CAG TCT CCA TCC TCC CTG TCT L4 (SEQ ID NO: 284)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GCC ATC CAG TTG ACC CAG TCT CCA TCC TCC CTG TCT L18 (SEQ ID NO: 285)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCA TCT TCC GTG TCT L5 (SEQ ID NO: 286)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !GAC ATC CAG ATG ACC CAG TCT CCA TCT TCT GTG TCT L19 (SEQ ID NO: 287)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !GAC ATC CAG TTG ACC CAG TCT CCA TCC TTC CTG TCT L8 (SEQ ID NO: 288)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GCC ATC CGG ATG ACC CAG TCT CCA TTC TCC CTG TCT L23 (SEQ ID NO: 239)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GCC ATC CGG ATG ACC CAG TCT CCA TCC TCA TTC TCT L9 (SEQ ID NO: 290)GCA TCT ACA GGA GAC AGA GTC ACC ATC ACT TGT  !GTC ATC TGG ATG ACC CAG TCT CCA TCC TTA CTC TCT L24 (SEQ ID NO; 291)GCA TCT ACA GGA GAC AGA GTC ACC ATC AGT TGT  !GCC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT L11 (SEQ ID NO: 292)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAC ATC CAG ATG ACC CAG TCT CCT TCC ACC CTG TCT L12 (SEQ ID NO: 293)GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC CTG CCC O11 (SEQ ID NO: 294)GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC CTG CCC O1 (SEQ ID NO: 295)GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !GAT GTT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC A17 (SEQ ID NO: 296)GTC ACC CTT GGA CAG CCG GCC TCC ATC TCC TGC  !GAT GTT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC A1 (SEQ ID NO: 297)GTC ACC CTT GGA CAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACC CAG ACT CCA CTC TCT CTG TCC A18 (SEQ ID NO: 293)GTC ACC CCT GGA CAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACC CAG ACT CCA CTC TCT CTG TCC A2 (SEQ ID NO: 299)GTC ACC CCT GGA CAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC A19 (SEQ ID NO: 300)GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC A3 (SEQ ID NO: 301)GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC TCA CCT A23 (SEQ ID NO: 302)GTC ACC CTT GGA CAG CCG GCC TCC ATC TCC TGC  !GAA ATT GTG TTG ACG CAG TCT CCA GGC ACC CTG TCT A27 (SEQ ID NO: 303)TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATT GTG TTG ACG CAG TCT CCA GCC ACC CTG TCT A11 (SEQ ID NO: 3CA)TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATA GTG ATG ACG CAG TCT CCA GCC ACC CTG TCT L2 (SEQ ID NO: 305)GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATA GTG ATG ACG CAG TCT CCA GCC ACC CTG TCT L16 (SEQ ID NO: 306)GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATT GTG TTG ACA CAG TCT CCA GCC ACC CTG TCT L6 (SEQ ID NO: 307)TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATT GTG TTG ACA CAG TCT CCA GCC ACC CTG TCT L20 (SEQ ID NO: 303)TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAA ATT GTA ATG ACA CAG TCT CCA GCC ACC CTG TCT L25 (SEQ ID NO: 30))TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !GAC ATC GTG ATG ACC CAG TCT CCA GAC TCC CTG GCT B3 (SEQ ID NO: 310)GTG TCT CTG GGC GAG AGG GCC ACC ATC AAC TGC  !GAA ACG ACA CTC ACG CAG TCT CCA GCA TTC ATG TCA B2 (SEQ ID NO: 311)GCG ACT CCA GGA GAC AAA GTC AAC ATC TCC TGC  !CAA ATT GTG CTG ACT CAG TCT CCA GAC TTT CAG TCT A26 (SEQ ID NO: 312)GTG ACT CCA AAG GAG AAA GTC ACC ATC ACC TGC  !GAA ATT GTG CTG ACT CAG TCT CCA GAC TTT CAG TCT A10 (SEQ ID NO: 313)GTG ACT CCA AAG GAG AAA GTC ACC ATC ACC TGC  !GAT GTT GTG ATG ACA CAG TCT CCA GCT TTC CTC TCT A14 (SEQ ID NO: 314)GTG ACT CCA GGG GAG AAA GTC ACC ATC ACC TGC  !

TABLE 9 RERS sites found in Human Kappa FR1 GLGs FokI HpyC MsII --> <----> PflFI BsrI BsmAI MnlI H4V VKI O12 1-69 3 3 23 12 49 15 18 47 26 36O2 101-169 103 103 123 112 149 115 118 147 126 136 O18 201-269 203 203223 212 249 215 218 247 226 236 O8 301-369 303 303 323 312 349 315 318347 326 336 A20 401-469 403 403 423 412 449 415 418 447 426 436 A30501-569 503 503 523 512 549 515 518 547 526 536 L14 601-669 603 603 612649 615 618 647 — 636 L1 701-769 703 703 723 712 749 715 718 747 726 736L15 801-869 803 803 823 812 849 815 818 847 826 836 L4 901-969 — 903 923912 949 906 915 918 947 926 936 L18 1001-1069 — 1003 1012 1049 1006 10151018 1047 1026 1036 L5 1101-1169 1103 — 1112 1149 1115 1118 1147 — 1136L19 1201-1269 1203 1203 1212 1249 1215 1218 1247 — 1236 L8 1301-1369 —1303 1323 1312 1349 1306 1315 1318 1347 — 1336 L23 1401-1469 1403 14031408 1412 1449 1415 1418 1447 — 1436 L9 1501-1569 1503 1503 1508 15231512 1549 1515 1518 1547 1526 1536 L24 1601-1669 1603 1608 1623 16121649 1615 1618 1647 — 1636 L11 1701-1769 1703 1703 1723 1712 1749 17151718 1747 1726 1736 L12 1801-1869 1803 1803 1812 1849 1815 1818 1847 —1836 VKII O11 1901-1969 — — — — — 1956 — O1 2001-2069 — — — — — 2056 —A17 2101-2169 — — 2112 — 2118 2156 — A1 2201-2269 — — 2212 — 2218 2256 —A18 2301-2369 — — — — — 2356 — A2 2401-2469 — — — — — 2456 — A192501-2569 — — 2512 — 2518 2556 — A3 2601-2669 — — 2612 — 2618 2656 — A232701-2769 — — — — — 2729 — VKIII A27 2801-2869 — — 2812 — 2818 2839 2860— A11 2901-2969 — — 2912 — 2918 2939 2960 — L2 3001-3069 — — 3012 — 30183039 3060 — L16 3101-3169 — — 3112 — 3118 3139 3160 — L6 3201-3.269 — —3212 — 3218 3239 3260 — L20 3301-3369 — — 3312 — 3318 3339 3360 — L253401-3469 — — 3412 — 3418 3439 3460 — VKIV B3 3501-3569 3503 — 3512 35153518 3539 3551< — VKV B2 3601-3669 — — 3649 — 3618 3647 — VKVI A263701-3769 — — 3712 — 3718 — A10 3801-3869 — — 3812 — 3818 — A143901-3969 — — 3912 — 3918 3930> —

TABLE 9 RERS sites found in Human Kappa FR1 GLGs, continued MaeIII HphIHpaII Tsp45I xx38 MspI MlyI same xx56 xx06 SfaNI SfcI HinfI --> --> <--sites xx62 xx52 VKI O12 1-69 37 41 53 53 55 56 — O2 101-169 137 141 153153 155 156 — O18 201-269 237 241 253 253 255 256 — O8 301-369 337 341353 353 355 356 — A20 401-469 437 441 453 453 455 456 — A30 501-569 537541 553 553 555 556 — L14 601-669 637 641 653 653 655 656 — L1 701-769737 741 753 753 755 756 — L15 801-869 837 841 853 853 855 856 — L4901-969 937 941 953 953 955 956 — L18 1001-1069 1037 1041 1053 1053 10551056 — L5 11014169 1137 1141 1153 1153 1155 1156 — L19 1201-1269 12371241 1253 1253 1255 1256 — L8 1301-1369 1337 1341 1353 1353 1355 1356 —L23 1401-1469 1437 1441 11453 1453 1455 1456 1406 L9 1501-1569 1537 5411553 1553 1555 1556 1506 L24 1601-1669 1637 1641 1653 1653 1655 1656 L111701-1769 1737 1741 1753 1753 1755 1756 L12 1801-1869 1837 1841 18531853 1855 1856 VKII O11 1901-1969 — — 1918 1918 1937 1938 1952 O12001-2069 — — 2018 2018 2037 2038 2052 A17 2101-2169 — — 2112 2112 21372138 2152 A1 2201-2268 — — 2212 2212 2237 2238 2252 A18 2301-2369 — —2318 2318 2337 2338 2352 A2 2401-2469 — — 2418 2418 2437 2438 2452 A192501-2569 — — 2512 2512 2537 2538 2552 A3 2601-2669 — — 2612 2612 26372638 2652 A23 2701-2769 — — 2718 2718 2737 2731* 2738* — VKIII A272801-2869 — — — — — A11 2901-2969 — — — — — L2 3001-3069 — — — — — L163101-3169 — — — — — L6 3201-3269 — — — — — L20 3301-3369 — — — — — L253401-3469 — — — — — VKIV B3 3501-3569 — — 3525 3525 — VKV B2 3601-3669 —— 3639 3639 — VKVI A26 3701-3769 — — 3712 3739 3712 3739 3737 3755 37563762 — A10 3801-3869 — — 3812 3839 3812 3839 3837 3855 3856 3862 — A143901-3969 — — 3939 3939 3937 3955 3956 3962 —

TABLE 9 RERS sites found in Human Kappa FR1, continued BpmI BsrFI BsaJIBssKI (NstNI) xx20 xx41 xx44 Cac8I NaeI xx29 xx42 xx43 xx22 xx30 xx43--> --> <-- NgoMIV HaeIII Tsp509I VKI O12 1-69 — — — — — — O2 101-169 —— — — — — O18 201-269 — — — — — — O8 301-369 — — — — — — A20 401-469 — —— — — — A30 501-569 — — — — — — L14 601-669 — — — — — — L1 701-769 — — —— — — L15 801-869 — — — — — — L4 901-969 — — — — — — L18 1001-1069 — — —— — — L5 1101-1169 — — — — — — L19 1201-1269 — — — — — — L8 1301-1369 —— — — — — L23 1401-1469 — — — — — — L9 1501-1569 — — — — — — L241601-1669 — — — — — — L11 1701-1769 — — — — — — L12 1801-1869 — — — — —— VKII O11 1901-1969 1942 1943 1944 1951 1954 — O1 2001-2069 2042 20432044 2051 2054 — A17 2101-2169 2142 — — 2151 2154 — A1 2201-2269 2242 —— 2251 2254 — A18 2301-2369 2342 2343 — 2351 2354 — A2 2401-2469 24422443 — 2451 2454 — A19 2501-2569 2542 2543 2544 2551 2554 — A3 2601-26692642 2643 2644 2651 2654 — A23 2701-2769 2742 — — 2751 2754 — VKIII A272801-2869 2843 2822 2843 2820 2841 — — 2803 A11 2901-2969 2943 2943 29202941 — — 2903 L2 3001-3069 3043 3043 3041 — — — L16 3101-3169 3143 31433120 3141 — — — L6 3201-3269 3243 3243 3220 3241 — — 3203 L20 3301-33693343 3343 3320 3341 — — 3303 L25 3401-3469 3443 3443 3420 3441 — — 3403VKIV B3 3501-3569 3529 3530 3520 — 3554 VKV B2 3601-3669 3643 3620 3641— — VKVI A26 3701-3769 — 3720 — — 3703 A10 3801-3869 — 3820 — — 3803 A243901-3969 3943 3943 3920 3941 — — —

TABLE 10 Lambda FR1 GLG sequences ! VL1CAG TCT GTG CTG ACT CAG CCA CCC TCG GTG TCT GAAGCC CCC AGG CAG AGG GTC ACC ATC TCC TGT ! 1a (SEQ ID No: 315)cag tct gtg ctg acG cag ccG ccc tcA gtg tct gGGgcc ccA Ggg cag agg gtc acc atc tcc tgC ! 1e (SEQ ID No: 316)cag tct gtg ctg act cag cca ccc tcA gCg tct gGGAcc ccc Ggg cag agg gtc acc atc tcT tgt ! 1c (SEQ ID NO: 317)cag tct gtg ctg act cag cca ccc tcA gCg tct gGGAcc ccc Ggg cag agg gtc acc atc tcT tgt ! 1g (SEQ ID NO: 318)cag tct gtg Ttg acG cag ccG ccc tcA gtg tct gCGgcc ccA GgA cag aAg gtc acc atc tcc tgC ! 1b (SEQ ID NO: 319) ! VL2CAG TCT GCC CTG ACT CAG CCT CCC TCC GCG TCC GGGTCT CCT GGA CAG TCA GTC ACC ATC TCC TGC ! 2c (SEQ ID NO: 320)cag tct gcc ctg act cag cct cGc tcA gTg tcc gggtct cct gga cag tca gtc acc atc tcc tgc! 2e (SEQ ID NO: 321)cag tct gcc ctg act cag cct Gcc tcc gTg tcT gggtct cct gga cag tcG Atc acc atc tcc tgc ! 2a2 (SEQ ID NO: 322)cag tct gcc ctg act cag cct ccc tcc gTg tcc gggtct cct gga cag tca gtc acc atc tcc tgc ! 2d (SEQ ID NO: 323)cag tct gcc ctg act cag cct Gcc tcc gTg tcT gggtct cct gga cag tcG Atc acc atc tcc tgc ! 2b2 (SEQ ID NO: 324) ! VL3TCC TAT GAG CTG ACT CAG CCA CCC TCA GTG TCC GTGTCC CCA GGA CAG ACA GCC AGC ATC ACC TGC ! 3r (SEQ ID NO: 325)tcc tat gag ctg act cag cca cTc tca gtg tcA gtgGcc cTG gga cag acG gcc agG atT acc tgT ! 3j (SEQ ID NO: 326)tcc tat gag ctg acA cag cca ccc tcG gtg tcA gtgtcc cca gga caA acG gcc agG atc acc tgc! 3p (SEQ ID NO: 327)tcc tat gag ctg acA cag cca ccc tcG gtg tcA gtgtcc cTa gga cag aTG gcc agG atc acc tgc ! 3a (SEQ ID NO: 328)tcT tCt gag ctg act cag GAC ccT GcT gtg tcT gtgGcc TTG gga cag aca gTc agG atc acA tgc ! 3l (SEQ ID NO: 329)tcc tat gTg ctg act cag cca ccc tca gtg tcA gtgGcc cca gga Aag acG gcc agG atT acc tgT ! 3h (SEQ ID NO: 330)tcc tat gag ctg acA cag cTa ccc tcG gtg tcA gtgtcc cca gga cag aca gcc agG atc acc tgc ! 3e (SEQ ID NO: 331)tcc tat gag ctg aTG cag cca ccc tcG gtg tcA gtgtcc cca gga cag acG gcc agG atc acc tgc ! 3m (SEQ ID NO: 332)tcc tat gag ctg acA cag cca Tcc tca gtg tcA gtgtcT ccG gga cag aca gcc agG atc acc tgc ! V2-19 (SEQ ID NO: 333) ! VL4CTG CCT GTG CTG ACT CAG CCC CCG TCT GCA TCT GCCTTG CTG GGA GCC TCG ATC AAg CTC ACC TGC ! 4c (SEQ ID NO: 334)cAg cct gtg ctg act caA TcA TcC tct gcC tct gcTtCC ctg gga Tcc tcg Gtc aag ctc acc tgc ! 4a (SEQ ID NO: 335)cAg cTt gtg ctg act caA TcG ccC tct gcC tct gcctCC ctg gga gcc tcg Gtc aag ctc acc tgc ! 4b (SEQ ID NO: 336) ! VL5CAG CCT GTG CTG ACT CAG CCA CCT TCC TCC TCC GCATCT CCT GGA GAA TCC GCC AGA CTC ACC TGC ! 5e (SEQ ID NO: 337)cag Gct gtg ctg act cag ccG Gct tcc CTc tcT gcatct cct gga gCa tcA gcc agT ctc acc tgc ! 5c (SEQ ID NO: 338)cag cct gtg ctg act cag cca Tct tcc CAT tcT gcatct Tct gga gCa tcA gTc aga ctc acc tgc ! 5b (SEQ ID NO: 339) ! VL6AAT TTT ATG CTG ACT CAG CCC CAC TCT GTG TCG GAGTCT CCG GGG AAG ACG GTA ACC ATC TCC TGC ! 6a (SEQ ID NO: 340) !VL7CAG ACT GTG GTG ACT CAG GAG CCC TCA CTG ACT GTGTCC CCA GGA GGG ACA GTC ACT CTC ACC TGT ! 7a (SEQ ID NO: 341)cag Gct gtg gtg act cag gag ccc tca ctg act gtgtcc cca gga ggg aca gtc act ctc acc tgt ! 7b (SEQ ID NO: 342) ! VL8CAG ACT GTG GTG ACC CAG GAG CCA TCG TTC TCA GTGTCC CCT GGA GGG ACA GTC ACA CTC ACT TGT ! 8a (SEQ ID NO: 343) ! VL9CAG CCT GTG CTG ACT CAG CCA CCT TCT GCA TCA GCCTCC CTG GGA GCC TCG GTC ACA CTC ACC TGC ! 9a (SEQ ID NO: 344) ! VL10CAG GCA GGG CTG ACT CAG CCA CCC TCG GTG TCC AAGGGC TTG AGA CAG ACC GCC ACA CTC ACC TGC ! 10a (SEQ ID NO: 345)

TABLE 11 RERSs found in human lambda FR1 GLGs ! There are 31 lambda GLGsMlyI NnnnnnGACTC (SEQ ID NO: 346) 25  1: 6  2: 6  4: 6  6: 6  7: 6  8: 6 9: 6 10: 6 11: 6 12: 6 15: 6 16: 6 20: 6 21: 6 22: 6 23: 6 23: 50 24: 625: 6 25: 50 26: 6 27: 6 28: 6 30: 6 21: 6 There are 23 hits at base# 6-″- GAGTCNNNNNn (SEQ ID NO: 347) 1 26: 34MwoI GCNNNNNnngc (SEG ID NO: 348) 20  1: 9  2: 9  3: 9  4: 9 11: 911: 56 12: 9 13: 9 14: 9 16: 9 17: 9 18: 9 19: 9 20: 9 23: 9 24: 9 25: 926: 9 30: 9 31: 9 There are 19 hits at base# 9 HinfI Gantc 27  1: 12 3: 12  4: 12  6: 12  7: 12  8: 12  9: 12 10: 12 11: 12 12: 12 15: 1216: 12 20: 12 21: 12 22: 12 23: 12 23: 46 23: 56 24: 12 25: 12 25: 5626: 12 26: 34 27: 12 28: 12 30: 12 31: 12 There are 23 hits at base# 12PleI gactc 2  1: 12  3: 12  4: 12  6: 12  7: 12  8: 12  9: 12 10: 1211: 12 12: 12 15: 12 16: 12 20: 12 21: 12 22: 12 23: 12 23: 56 24: 1225: 12 25: 56 26: 12 27: 12 28: 12 30: 12 31: 12There are 23 hits at base# 12 -″- gagtc 26: 34 DdeI Ctnag 32  1: 14 2: 24  3: 14  3: 24  4: 14  4: 24  5: 24  6: 14  7: 14  7: 24  8: 14 9: 14 10: 14 11: 14 11: 24 12: 14 12: 24 15: 5 15: 14 16: 14 16: 2419: 24 20: 14 23: 14 24: 14 25: 14 26: 14 27: 14 28: 14 29: 30 30: 1431: 14 There are 21 hits at base# 14 B3aJI Ccnngg 38  1: 23  1: 40 2: 39  2: 40  3: 39  3: 40  4: 39  4: 40  5: 39 11: 39 12: 38 12: 3913: 23 13: 39 14: 23 14: 39 15: 38 16: 39 17: 23 17: 39 18: 23 18: 3921: 38 21: 39 21: 47 22: 38 22: 39 22: 47 26: 40 27: 39 28: 39 29: 1429: 39 30: 38 30: 39 30: 47 31: 23 31: 32 There are 17 hits at base# 39There are 5 hits at base# 38 There are 5 hits at base# 40 Makes cleavageragged. MnlI cctc 3  1: 23  2: 23  3: 23  4: 23  5: 23  6: 19  6: 23 7: 19  8: 23  9: 19  9: 23 10: 23 11: 23 13: 23 14: 23 16: 23 17: 2313: 23 19: 23 20: 47 21: 23 21: 29 21: 47 22: 23 22: 29 22: 35 22: 4723: 26 23: 29 24: 27 27: 23 28: 23 30: 35 30: 47 31: 23There are 21 hits at base# 23 There are 3 hits at base# 19There are 3 hits at base# 29 There are 1 hits at base# 26There are 1 hits at base# 27 These could make cleavage ragged.-″- gagg 7  1: 48  2: 48  3: 48  4: 48 27: 44 28: 44 29: 44BssKI Nccngg 39  1: 40  2: 39  3: 39  3: 40  4: 39  4: 40  5: 39  6: 31 6: 39  7: 31  7: 39  8: 39  9: 31  9: 39 10: 39 11: 39 12: 38 12: 5213: 39 13: 52 14: 52 16: 39 16: 52 17: 39 17: 52 18: 39 18: 52 19: 3919: 52 21: 38 22: 38 23: 39 24: 39 26: 39 27: 39 28: 39 29: 14 29: 3930: 38 There are 21 hits at base# 39 There are 4 hits at base# 38There are 3 hits at base# 31 There are 3 hits at base# 40 RaggedBstNI CCwgg 30  1: 41  2: 40  5: 40  6: 40  7: 40  8: 40  9: 40 10: 4011: 40 12: 39 12: 53 13: 40 13: 53 14: 53 16: 40 16: 53 17: 40 17: 5318: 40 18: 53 19: 53 21: 39 22: 39 23: 40 24: 40 27: 40 28: 40 29: 1529: 40 30: 39 There are 17 hits at base# 40 There are 7 hits at base# 53There are 4 hits at base# 39 There are 1 hits at base# 41 RaggedPspGI ccwgg 30  1: 41  2: 40  5: 40  6: 40  7: 40 8 : 40  9: 40 10: 4011: 40 12: 39 12: 53 13: 40 13: 53 14: 53 16: 40 16: 53 17: 40 17: 5318: 40 18: 53 19: 53 21: 39 22: 39 23: 40 24: 40 27: 40 28: 40 29: 1529: 40 30: 39 There are 17 hits at base# 40 There are 7 hits at base# 53There are 4 hits at base# 39 There are 1 hits at base# 41 ScrFI CCngg 39 1: 41  2: 40  3: 40  3: 41  4: 40  4: 41  5: 40  6: 32  6: 40  7: 32 7: 40  8: 40  9: 32  9: 40 10: 40 11: 40 12: 39 12: 53 13: 40 13: 5314: 53 16: 40 16: 53 17: 40 17: 53 18: 40 18: 53 19: 40 19: 53 21: 3922: 39 23: 40 24: 40 26: 40 27: 40 28: 40 29: 15 29: 40 30: 39There are 21 hits at basei 40 There are 4 hits at base# 39There are 3 hits at base# 41 MaeIII gtnac 16  1: 52  2: 52  3: 52  4: 52 5: 52  6: 52  7: 2  9: 52 26: 52 27: 10 27: 52 28: 10 28: 52 29: 1029: 52 30: 52 There are 13 hits at base# 52 Tsp45I gtsac 15  1: 52 2: 52  3: 52  4: 52  5: 52  6: 52  7: 52  9: 52 27: 10 27: 52 28: 1028: 52 29: 10 29: 52 30: 52 There are 12 hits at base# 52 HphI tcacc 26 1: 53  2: 53  3: 53  4: 53  5: 53  6: 53  7: 53  8: 53  9: 53 10: 5311: 59 13: 59 14: 59 17: 59 18: 59 19: 59 20: 59 21: 59 22: 59 23: 5924: 59 25: 59 27: 59 28: 59 30: 59 31: 59 There are 16 hits at base# 59There are 10 hits at base# 53 BspMI ACCTGCNNNNn (SEQ ID NO: 349) 1411: 61 13: 61 14: 61 17: 61 18: 61 19: 61 20: 61 21: 61 22: 61 23: 6124: 61 25: 61 30: 61 31: 61 There are 14 hits at base# 61 Goes into CDR1

TABLE 12 Matches to URE FR3 adapters in 79 human HC.A. List of Heavy-chains genes sampled AF008566 af103343 HSA235676HSU94412 MCOMFRAA AF035043 AF103367 HSA235675 HSU94415 MCOMFRVA AF103026AF103368 HSA235674 HSU94416 S32745 af103033 AF103369 HSA235673 HSU94417382764 AF103061 AF103370 HSA240559 HSU94413 S83240 Af103072 af103371HSCB201 HSU96389 SABVH369 af103078 AF103372 HSIGGVHC HSU96391 SADEIGVHAF103099 AF158381 HSU44791 HSU96392 SAH2TGVH AF103102 E05213 HSU44793HSU96395 SDA3IGVH AF103103 E05886 HSU82771 HSZ93849 SIGVHTTD AF103174E05887 HSU82949 HSZ93850 SUK4IGVH AF103186 HSA235661 HSU82950 HSZ93851af103187 HSA235664 HSU82952 HS3Z93853 AF103195 HSA235660 HSU82961HSZ93855 af103277 HSA235659 HSU36522 HS393357 af103286 HSA235678HSU86523 HSZ93860 AF103309 HSA235677 HSU92452 HSZ93863Table 12B. Testing all distinct GLGs from bases 89.1 to 93.2 ofthe heavy variable domain Id NO: Nb 0 1 2 3 4 SEQ ID 1 30 15 11 10 0 2Seq1 gtgtattactgtgc 25 2 19 7 6 4 2 0 Seq2 gtAtattactgtgc 26 3 1 0 0 1 00 Seq3 utgtattactgtAA 27 4 7 1 5 1 0 0 Seq4 gtgtattactgtAc 28 5 0 0 0 00 0 Seq5 Ttgtattactatac 29 6 0 0 0 0 0 0 Seq6 TtgtatCactgtgc 30 7 3 1 01 1 0 Seq7 ACAtattactgtgc 31 8 2 0 2 0 0 0 Seq8 ACgtattactutac 32 9 9 22 4 1 0 Seq9 ATgtattactatac 33 Group 26 26 21 4 2 Cumulative 26 5 73 7779 Table 12C Most important URE recognition secTs in FRS Heavy 1 VHSzy1GTGtattactgtgc (ON_SHC103) (SEQ ID NO: 25) 2 VHSzy2 GTAtattactgtgc(ON_SHC323) (SEQ ID NO: 28) 3 VHSzy4 GTGtattactgtac (ON_SHC349)(SEQ ID NO: 28) 4 VHSzy9 ATGtattactgtgc (ON_SHC5a) (SEQ ID NO: 33)Table 12D, testing 79 human HC V genes with four probesNumber of sequences . . . 79 Number of bases . . .  29143Number of mismatches Id Best 0 1 2 3 4 5 1 39 15 11 10 1 2 0 Seq1gtgtattactgtgc (SEQ ID NO: 25) 2 22 7 6 5 3 0 1 Seq2 atAtattactgtgc(SEQ ID NO: 26) 3 7 1 5 1 0 0 0 Seq4 gtgtattactgtAc (SEQ ID NO: 28) 4 112 4 4 1 0 0 Seq9 ATgtattactgtgc (SEQ ID NO: 33) Group 25 26 20 5 2Cumulative 25 51 71 76 78 One sequence has five mismatches withsequences 2, 4, and 9; it is scored as best for 2. Id is the number ofthe adapter. Best is the number of sequence for which the identifiedadapter was the best available. The rest of the table shows how well thesequences match the adapters. For example, there are 10 sequences thatmatch VHSzy1(Id = 1) with 2 mismatches and are worse for all otheradapters. In this sample, 90% come within 2 bases of one of the fouradapters.

TABLE 13 The following list of enzymes was taken fromrebase.neb.com/cgi-bin/asymmlist.I have removed the enzymes that a) cut within the recognition, b) cut onboth sides of the recognition, or c) have fewer than 2 bases betweenrecognition and closest cut site. REBASE Enzyme Apr./13/2001Type II restriction enzymes with asymmetric recognition sequences:Enzymes Recognition Sequence Isoschizomers Suppliers AarICACCTGCNNNN{circumflex over ( )}NNNN_ — y AceIIICAGCTCNNNNNNN{circumflex over ( )}NNNN_ — — BbrVIGAAGACNNNNNNN{circumflex over ( )}NNNN_ — — BbvIGCAGCNNNNNNNN{circumflex over ( )}NNNN_ y BbvII GAAGACNN{circumflex over( )}NNNN_ Bce831 CTTGAGNNNNNNNNNNNNNN_NN{circumflex over ( )} — — BceAIACGGCNNNNNNNNNNN{circumflex over ( )}NN_ — y BcefIACGGCNNNNNNNNNNN{circumflex over ( )}N_ — — BciVIGTATCCNNNNN_N{circumflex over ( )} BfuI y BfiI ACTGGGNNNN_N{circumflexover ( )} BmrI y BinI GGATCNNNN{circumflex over ( )}N_ BscAIGCATCNNNN{circumflex over ( )}NN_ — — BseRI GAGGAGNNNNNNNN_NN{circumflexover ( )} — y BsmFI GGGACNNNNNNNNNN{circumflex over ( )}NNNN_ BspLU11IIIy BspMI ACCTGCNNNN{circumflex over ( )}NNNN_ Acc36I y EciIGGCGGANNNNNNNNN_NN{circumflex over ( )} — y Eco57ICTGAAGNNNNNNNNNNNNNN_NN{circumflex over ( )} BspKT5I y FauICCCGCNNNN{circumflex over ( )}NN_ BstFZ438I y FokIGGATGNNNNNNNNN{circumflex over ( )}NNNN_ Bstpz4181 y GsuICTGGAGNNNNNNNNNNNNNN_NN{circumflex over ( )} — y HgaIGACGCNNNNN{circumflex over ( )}NNNNN_ — y HphI GGTGANNNNNNN_N{circumflexover ( )} AsuHPI y MboII GAAGANNNNNNN_N{circumflex over ( )} — y MlyIGAGTCNNNNN{circumflex over ( )} SchI y MmeITCCRACNNNNNNNNNNNNNNNNNN_NN{circumflex over ( )} — — MnlICCTCNNNNNN_N{circumflex over ( )} — PleI GAGTCNNNN{circumflex over( )}N_ PpsI y RleAI CCCACANNNNNNNNN_NNN{circumflex over ( )} — — SfaNIGCATCNNNN{circumflex over ( )}NNNN_ BspST5I y SspD5IGGTGANNNNNNNN{circumflex over ( )} — — Sth132I CCCGNNNN{circumflex over( )}NNNN_ — — StsI GGATGNNNNNNNNNN{circumflex over ( )}NNNN_ — — TaqIIGACCGANNNNNNNNN_NN{circumflex over ( )}, CACCCANNNNNNNNN_NN{circumflexover ( )} — — Tth111II CAARCANNNNNNNNN_NN{circumflex over ( )} — — UbaPICGAACG — — (SEQ ID NOs: 356-390, respectively, in order of appearance)The notation is {circumflex over ( )} means cut the upper strand and _means cut the lower strand. If the upper and lower strand are cut at thesame place, then only {circumflex over ( )} appears.

TABLE 14 (FOKlact) 5′-

 TTgTT 

-3′ (SEQ ID NO: 350) (VHEx881)5′-AATAgTAgAc TgcAgTgTcc TcAgcccTTA AgcTgTTcAT cTgcAAgTAg-AgAgTATTcT TAgAgTTgTc TcTAgAcTTA gTgAAgcg-3′ (SEQ ID NO: 351)! note that VHEx881 is the reverse complement cf the ON below ![RC] 5′-cgCttcacTaag- !         Scab . . .  !        Synthetic 3-23 as in Table 206 !        |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- !        XbaI . . .  !        |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|t-3′ (SEQ ID NO: 352)!                AflII . . .  (VHBA881) 5′-cgCttcacTaag-   |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-   |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt gcg ag-3′ (SEQ ID NO: 353)(VHBB881) 5′-cgCttcacTaag-   |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-   |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt Acg ag-3′ (SEQ ID NO: 354)(VH881PCR) 5′-cgCttcacTaag|TCT|AGA|gac|aac -3′ (SEQ ID NO: 355)

TABLE 15 Use of FokI as “Universal Restriction Enzyme”FokI - for dsDNA, | represents sites of cleavage               sites of cleavage5′-cacGGATGtg--nnnnnnn|nnnnnnn-3′(SEQ ID NO: 15)3′-gtgCCTACac--nnnnnnnnnnn|nnn-5′ (SEQ ID NO: 16)     RECOG    NITion of FokI Case I

Case II

Case III (Case I rotated 180 degrees)

Case IV (Case II rotated 180 degrees)

Improved FokI adapters FokI - for dsDNA, | represents sites of cleavageCase I Stem 11, loop 5, stem 11, recognition 17

Case II Stem 10, loop 5, stem 10, recognition 18

Case III (Case I rotated 180 degrees)Stem 11, loop 5, stem 11, recognition 20

Case IV (Case II rotated 180 degrees)Stem 11, loop 4, stem 11, recognition 17

BseRI  (SEQ ID NO: 9)     | sites of cleavage5′-cacGAGGAGnnnnnnnnnn|nnnnn-3′ 3′-gtgctctcctcnnnnnnnn|nnnnnnn-5′    RECOG     NITion of BseRI Stem 11, loop 5, stem 11, recognition 19

TABLE 16 Human heavy chains bases 88.1 TO 94.2Number of sequences . . . 840 Number of Mismatchers . . .  Probe Id Ntot0 1 2 3 4 5 6 7 Name Sequence . . .  Dot form . . .   1 364 152 97 76 267 4 2 0 VHS881-1.1 gctgtgtattactgtgcgag gctgtgtattactgtgcgag  2 265 15060 33 13 5 4 0 0 VES881-1.2 gccgtgLattactgtgogag ..c.................  396 14 34 16 10 5 7 9 1 VBS881-2.1 gccgtatattactgtgcgag..c..a.............. 20 0 3 4 9 2 2 0 0 V5S881-4.1 gccgtgtattactgtacgag..c............a.... 95 25 36 18 11 2 2 0 1 VHS881-9.1gccatgtattactqtgcgag ..ca................ 840 341 230 147 69 21 19 11 2(SEQ. ID NOs: 391-395, respectively in order of 341 571 718 787 808 827838 840 appearance) 88 89 90 91 92 93 94 95 Codon number as in Table 195Recognition . . .  Stem . . .  Loop . . .  Stem . . .  (VHS881-1.1)5′-gctgtgtat|tact-gtgcgag

TTgTT

-3′ (VHS881-1.2) 5′-gccgtgtat|tact-gtgcgag

TTgTT

-3′ (VHS881-2.1) 5′-gccgtatat|tact-gtgcgag

TTgTT

-3′ (VHS881-4.1) 5′-gcagtgtat|tact-gtacgag

TTgTT

-3′ (VHS881-9.1) 5′-gccatgtat|tact-gtgcgag

TTgTT

-3′ | site of substrate cleavage(Sequences in the left column above are SEQ. ID NOs 391-395, respectively in oder of appearance;Sequences in the right column above are all SEQ ID NO: 396) (FOKlact)5′-

 TTgTT 

-3′ (SEQ ID NO: 396) (VHEx881)5′-AATAgTAgAc TgcAgTgTcc TcAgcccTTA AgcTgTTcAT cTgcAAgTAg-AgAgTATTcT TAgAgTTgTc TcTAgAcTTA gTgAAgcg-3′ (SEQ ID NO: 397)! note that VHEx881 is the reverse complement of the ON below ![RC] 5′-cgCttcacTaag- !     Scab . . .  !    Synthetic 3-23 as in Table 206 !    |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- !    XbaI . . .  !    |aac|agC|TTA|AGg|gcg|gag|gac|aCT|GCA|Gtc|tac|tat|t-3′ !   AflII . . .  (VHBA881)    5′-cgCttcacTaag-|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-|aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt gcg ag-3′ (SEQ ID NO: 398)(VHBB881)    5′-cgCttcacTaag-|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-|aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt Acg ag-3′ (SEQ ID NO: 618)  (VH881PCR) 5′-cgCttcacTaag|TCT|AGA|gac|aac -3′ (SEQ ID NO: 399)

TABLE 17  Kappa, bases 12-30 !! ID Ntot  0  1  2  3  4  5  6  Name    Sequence........... Dot Form........... ! 1   84   40 21 20 1  2  0  0  SK12O12 gacccagtctccatcctcc gacccagtctccatcctcc (residues 26-44 of SEQ ID NO: 400)! 2   32   19  3  6 2  1  0  1  SK12A17 gactcagtctccactctcc ...t.........ct.... (residues 26-44 of SEQ ID NO: 400)! 3   26   17  8  1 0  0  0  0  SK12A27 gacgcagtctccaggcacc ...g.........gg..a.. (residues 26-44 of SEQ ID NO: 400)! 4   40   21 18  1 0  0  0  0  SK12A11 gacgcagtctccagccacc ...g.........g..a.. (residues 26-44 of SEQ ID NO: 400)!    182   97 50 28 3  3  0  1 !       97 147 175 178 181 181 182 !URE adapters:!            Stem...... Loop. Stem...... Recognition.......(SzKB1230-O12)     5′-cAcATccgTg TTgTT cAcggATgTg ggAggATggAgAcTgggTc-3′ (SEQ ID NO: 400)!       [RC] 5′-gacccagtctccatcctcc 

 AAcAA 

-3′ !            Recognition........ Stem...... loop. Stem......!                             FokI.           FokI. !!            Stem...... Loop. Stem...... Recognition.......(SzKB1230-A17)     5′-cAcATccgTg TTgTT cAcggATgTg ggAgAgTggAgAcTgAgTc-3′ (SEQ ID NO: 401)!       [RC] 5′-gactcagtctccactctcc 

 AAcAA 

-3′ !            Recognition........ Stem...... loop. Stem......!                             FokI.           FokI.!            Stem...... Loop. Stem...... Recognition.......(SzKB1230-A27)     5′-cAcATccgTg TTgTT cAcggATgTg ggTggccTggAgAcTgcgTc-3′ (SEQ ID NO: 402)!       [RC] 5′-gacgcagtctccaggcacc 

 AAcAA 

-3′ !            Recognition........ Stem...... loop. Stem......!                             FokI.           FokI. !!            Stem...... Loop. Stem...... Recognition.......(SzKB1230-A11)      5′-cAcATccgTg TTgTT cAcggATgTg ggTggcTggAgAcTgcgTc-3′ (SEQ ID NO: 403)!       [RC] 5′-gacgcagtctccagccacc 

 AAcAA 

-3′ !            Recognition........ Stem...... loop. Stem......!                             FokI.           FokI.What happens in the upper strand: (SzKB1230-O12*) ! ! (SzKB1230-A17*) !(SzKB1230-A27*) ! (SzKB1230-A11*) (kapextURE) (kapextUREPCR)(kaBR01UR)   5′-ggAggATggA cTggATgTct TgTgcAcTgT gAcAAgAgTA gAgg-3′ (SEQ ID NO: 406)!       [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-tc ctc c-3′ ON above is R.C. of this one(kaBR02UR)   5′-ggAggATggA cTggATgTct TgTgcAcTgT gAcAAgAgTA gAgg-3′ (SEQ ID NO: 407)!       [RC] 5′-ggTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-ct ctc c-3′ ON above is R.C. of this one(kaBR03UR)   5′-ggTgccTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ (SEQ ID NO: 408)!       [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gg cac c-3′ ON above is R.C. of this one(kaBR04UR)   5′-ggTggcTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ (SEQ ID NO: 409)!       [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gc cac c-3′ ON above is R.C. of this one               Scab..............ApaLI.

TABLE 18 Lambda URE adgpters bases 13.3 to 19.3 ! ! Number of sequences.......... 128  ! !      Number of mismatches..............! Id Ntot 0 1  2 3 4 5  6  7 8 Name      Sequence........... Dot form...........! 1  58  45 7  1 0 0 0  2  2 1 VL133-2a2 gtctcctggacagtcgatc gtctcctggacagtcgatc (residues 632-635 of SEQ ID NO: 410) ! 2  16  10 1  0 1 0 1  1  0 2 VL133-3l  ggccttgggacagacagtc .g.cttg......a.ag.. (residues 632-635 of SEQ ID NO: 411) ! 3  17   6 0  0 0 4 1  1  5 0 VL133-2c  gtctcctggacagtcagtc ...............ag.. (residues 632-635 of SEQ ID NO: 412) ! 4  37   3 0 10 4 4 3  7  4 2 VL133-1c  ggccccagggcagagggtc .g.c..a..g...ag.g.. (residues 632-635 of SEQ ID NO: 413) !   128  64 8 11 5 8 5 11 11 5        64 72 83 88 96 101 112 123 128 !          Stem...... loop. Stem...... Recognition........ (VL133-2a2) 5′-cAcATccgTg TTgTT cAcggATgTg gATcgAcTgTccAggAgAc-3′ (SEQ ID NO: 410) !     [RC] 5′-gtctcctggacagtcgatc 

 AAcAA 

-3′  !          Recognition........ Stem...... loop. Stem...... ! !          Stem...... loop. Stem...... Recognition........ (VL133-3l) 5′-cAcATccgTg TTgTT cAcggATgTg gAcTgTcTgTcccA Aggcc-3' (SEQ ID NO: 411) !    [RC] 5′-ggccttgggacagacagtc 

 AAcAA 

-3′  !         Recognition........ Stem...... loop. Stem...... ! !          Stem...... loop. Stem...... Recognition........ (VL133-2c) 5′-cAcATccgTg TTgTT cAcggATgTg gAcTgAcTgTccAggAgAc-3′ (SEQ ID NO: 412) !    [RC] 5′-gtctcctggacagtcagtc 

 AAcAA 

-3′ !         Recognition........ Stem...... loop. Stem...... ! !          Stem...... loop. Stem...... Recognition........ (VL133-1c) 5′-cAcATccgTg TTgTT cAcggATgTg gAcccTcTgcccTggggcc-3′ (SEQ ID NO: 413)      [RC] 5′-ggccccagggcagagggtc 

 AAcAA 

-3' What happens in the top strand: !                 | site of cleavage in the upper strand (VL133-2a2*) 5′-g tct cct g|ga cag tcg atc (residues 632-635 of SEQ ID NO: 410) ! (VL133-3l*) 5′-g gcc ttg g|ga cag aca gtc (residues 632-635 of SEQ ID NO: 411) !(VL133-2c*) 5'-g tct cct g|ga cag tca gtc (residues 632-635 of SEQ ID NO: 412) ! (VL133-1e) 5'-g gcc cca g|gg cag agg gtc (residues 632-635 of SEQ ID NO: 413) ! ! The following Extenders and Bridges all encode the AA sequence of 2a2 for codons 1-15 !                  1  (ON_LamEx133) 5′-ccTcTgAcTgAgT gcA cAg-  ! !     2 3  4  5 6  7  8  9  10 11 12       AGt gcT TtA acC caA ccG gcT AGT gt-T AGC ggT-  ! !     13  14 15       tcC ccG g! 2a2 (SEQ ID NO: 414)  !(ON_LamB1-133)[RC] 5′-ccTcTgAcTgAgT gcA cAg - !     2 3  4  5 6  7  8  9  10 11 12       AGt gcT TtA acC caA ccG gcT AGT gsT AGC ggT-  ! !     13  14 15       tcC ccG g ga cag tcg at-3′ ! (SEQ ID NO: 415)_2a2 

 the actual seq is the !                           reverse complement of the !                           one shown.  !(ON_LamB2-133)[RC] 5′-ccTcTgAcTgAgT gcA cAg-  ! !     2 3  4  5 6  7   8 9  10 11 12       AGt gcT TtA acC caA ccG gcT AGT grT AGC ggT-  ! !     13  14 15       tcC ccG g ga cag aca gt-3′! (SEQ ID NO: 416) 31 N.B. the actual seq is the !                           reverse complement of the !                           one shown.  ! ! (ON_LamB3 133)[RC] 5′ ccTcTgAcTgAgT gcA cAg !     2 3  4  5  6  7  8 9  10 11 12       AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT-  ! !     13  14  15       tcC ccG g ga cag tca gt-3′! (SEQ ID NO: 417)_2c 

 the actual seq is the                              reverse complement of the                              one shown.  !! (ON_LamB4-133)      [RC]   5′-ccTcTgAcTgAgT gcA cAg-  ! !      2   3   4   5   6   7   8   9   10  11  12       AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT-s  !        13  14  15       tcC ccG g gg cag agg gt-3′ ! (SEQ ID NO: 413) 1c 

 the  actual seq is the !                                        reverse complement of the !                                        one shown.  ! (ON_Lam133PCR) 5′-ccTcTgAcTaAgT gcA cAg AGt gc-3′ (SEQ ID NO: 419) 

TABLE 19  Cleavage of 75 human light chains. Enzyme Recognition* Nch NsPlanned location of site AfeI AGCgct 0 0 AflII Cttaag 0 0 HC FR3 AgeIAccggL 0 0 AscI GGcgcgcc 0 0 After LC BglII Aqatct 0 0 BsiWI Cgtacg 0 0BspDI ATcgat 0 0 BssHII Gcgcgc 0 0 BstBI TTcgaa 0 0 DraIII CACNNNgtg 0 0EagI Cqqccg 0 0 FseI GGCCGGcc 0 0 FspI TGCgca 0 0 HpaI GTTaac 0 0 MfeICaattg 0 0 HC FR1 MluI Acgcgt 0 0 NcoI Ccatgg 0 0 Heavy chain signalNheI Gctagc 0 0 HC/anchor linker NotI GCggccgc 0 0 In linker after HCNruI TCGcga 0 0 PacI TTAATtaa 0 0 PmeI GTTTaaac 0 0 PmlI CACgtg 0 0 PvuICGATcg 0 0 SacII CCGCgg 0 0 SalI Gtcgac 0 0 SfiI GGCCNNNNnggcc 0 0Heavy Chain signal  (SEQ ID NO: 436) SgfI GCGATcgc 0 0 SnaBI TACgta 0 0StuI AGGcct 0 0 XbaI Tctaga 0 0 HC FR3 AatII GACGTc 1 1 AclI AAcgtt 1 1AseI ATtaat 1 1 BsmI GAATGCN 1 1 BspEI Tccgga 1 1HC FR1 (SEQ ID NO: 437) BstXI CCANNNNNntgg I 1 HC FR2 (SEQ ID NO: 438)DrdI GACNNNNnngtc 1 1 HindIII Aagctt 1 1 PciI Acatgt 1 1 SapI gaagagc 11 ScaI AGTact 1 1 SexAI Accwggt 1 1 SpeI Actagt 1 1 TliI Ctcgag 1 1 XhoICtcgag 1 1 BcgI cgannnnnntgo 2 2 (SDQ ID NO: 439) BlpI GCtnagc 2 2 BssSICtagtg 2 2 BstAPT GCANNNNntgc 2 2 (SEQ ID NO: 440) EspI GCtnagc 2 2 KasIGgcgcc 2 2 PflMI CCANNNNntgg 2 2 (SEQ ID NO: 441) XmnI GAANNnnttc 2 2(SEQ ID NO: 442) ApaLI Gtgcac 3 3 LC signal seq NaeI GCCggc 3 3 NgoMIGccggc 3 3 PvuII CAGctg 3 3 RsrII CGgwocg 3 3 BsrBI GAGcgg 4 4 BsrDIGCAATGNNn 4 4 BstZ17I GTAtac 4 4 EcoRI Gaattc 4 4 SphI GCATGc 4 4 SspIAATatt 4 4 AccI GTmkac 5 5 BclI Tgatca 5 5 BsmBI Nnnnnngagacg 5 5(SEQ ID NO: 443) BsrGI Tgtaca 5 5 DraI TTTaaa 6 6 NdeI CAtatg 6 6 HC FR4SwaI ATTTaaat 6 t BamHI Ggatcc 7 7 SacI GAGCTc 7 7 BciVI GTATCCNNNNUN 88 (SEQ ID NO: 444) BsaBI GATNNnnatc 8 8 (SEQ ID NO: 619) NsiI ATGCAt 8 8Bsp120I Gggccc 9 9 CH1 ApaI GGGCCc 9 9 CH1 PspOOMI Gggccc 9 9 BspHITcatga 9 11 EcoRV GATatc 9 9 AhdI GACNNNnngtc 11 11 (SEQ ID NO: 445)BbsI GAAGAC 11 14 PsiI TTAtaa 12 12 BsaI GGTCTCNnnnn 13 15(SEQ ID NO: 446) XmaI Cccggg 13 14 AvaI Cycgrg 14 16 BglI GCCNNNNnggc 1417 (SEQ ID NO: 447) AlwNI CAGNNNctg 16 16 BspMI ACCTGC 17 19 XcmICCANNNNNnnnntgg 17 26 (SEQ ID NO: 448) BstEII Ggtnacc 19 22 HC FR4Sse8387I CCTGCAgg 20 20 AvrII Cctagg 27 27 HincII GTYrac 22 22 BsgIGTGCAG 27 29 MscI TGGcca 30 34 BseRI NNnnnnnnnnctcctc 32 35(SEQ ID NO: 449) Bsu36I CCtnagg 35 37 PstI CTGCAg 35 40 EciInnnnnnnnntccgcc 38 40 (SEQ ID NO: 450) PpuMI RGgwccy 41 50 StyI Ccwwgg44 73 EcoO109I RGgnccy 46 70 Acc65I Ggtacc 50 51 KpnI GGTACc 50 51 BpmIctccag 53 82 AvaII Ggwcc 71 124 * cleavage occurs in the top strandafter the last upper-case base. For EMs that cut palindromic sequences,the lower strand is cut at the symmetrical site.

TABLE 20  Cleavage of 79 human heavy chains Planned location  EnzymeRecognition Nch Ns of site AfeI AGCgct 0 0 AflII Cttaag 0 0 NC FR3 AscIGGcgcgcc 0 0 After LC BsiWI Cgtacg 0 0 BspDI ATcgat 0 0 BssHII Gcgcgc 00 FseI GGCCGGcc 0 0 HpaI GTTaac 0 0 NheI Gctagc 0 0 HC Linker NotIGCggccgc 0 0 In linker, HC/anchor NruI TCGcga 0 0 NsiI ATGCAt 0 0 PacITTAATtaa 0 0 PciI Acatgt 0 0 PmeI GTTTaaac 0 0 PvuI CGATcg 0 0 RsrIICGgwccg 0 0 SapI aaagagc 0 0 SfiI GGCCNNNNnggcc 0 0 HC signal seq (SEQ ID NO: 420) SgfI GCGATcgc 0 0 SwaI ATTTaaat 0 0 Roil kAcgtt 1 1AgeI Accggt 1 1 AseI ATtaat 1 1 AvrII Cctagg 1 1 BsmI GAATGCN 1 1 BsrBIGAGcqg 1 1 BsrDI GCAATGNNn 1 1 Dual TTTaaa 1 1 FspI TGCgca 1 1 HindIIIAagctt 1 1 MfeI Caattg 1 1 HC FR1 NaeI GCCggc 1 1 NgoMI Gccggc 1 1 SpeIActagt 1 1 Acc65I Ggtacc 2 2 BstBI TTcgaa 2 2 KpnI GGTACc 2 2 MluIAcgcgt 2 2 NcoI Ccatgg 2 2 In HC signal seq NdeI CAtatg 2 2 HC FR4 PmlICACgtg 2 2 XcmI CCANNNNNnnnntgg 2 2 (SEQ ID NO: 421) BcgI cgannnnnntgc 33 (SEQ ID NO: 422) BclI Tgatca 3 3 BglI GCCNNNNnggc 3 3 (SEQ ID NO: 423)BsaBI GATNNnnatc 3 3 (SEQ ID NO: 424) BsrGI Tgtaca 3 3 SnaBI TACgta 3 3Sse8387I CCTGCAgg 3 3 ApaLI Gtgcac 4 4 LC Signal/FR1 BspHI Tcatga 4 4BssSI Ctcgtg 4 4 Pail TTAtaa 4 5 SpnI GCATGc 4 4 AhdI GACNNNnngtc 5 5(SEQ ID NO: 425) BspEI Tccgga 5 5 HC FR1 MscI TGGcca 5 5 SacI GAGCTc 5 5ScaI AGTact SexAI Accwggt 5 6 SspI AATatt 5 5 TliI Ctcgag 5 5 XhoICtcgag 5 5 BbsI GAAGAC 7 P BstAPI GCANNNNntgc 7 8 (SEQ ID NO: 426)BstZ17I GTAtac 7 7 BcoRV GATatc 7 7 EcoRI Gaattc 8 8 BlpI GCtnagc 9 9Bsu361 CCtnagg 9 9 DraIII CACNNNgtg 9 9 EspI GCtnagc 9 9 StuI AGGcct 913 XbaI Tctaga 9 9 HC FR3 Bsp120I Gggccc 10 11 CH1 ApaI GGGCCc 10 11 CH1PspOOMI Gggccc 10 ii BciVI GTATCCNNNNNN 11 11 (SEQ ID NO: 427) SalIGtcgac 11 12 DrdI GACNNNNnngtc 12 12 (SEQ ID NO: 428) KasI Ggcgcc 12 12XmaI Cccggg 12 14 BglII Agatct 14 14 HincII GTYrac 16 18 BamBI Ggatcc 1717 Pf1MI CCANNNNntgg 17 18 (SEQ ID NO: 429) BsmBI Nnnnnngagag 18 21(SEQ ID NO: 430) BstXI CCANNNNNntgg 18 19 HC FR2  (SEQ ID NO: 431) XmnIGAANNnnttc 18 18 (SEQ ID NO: 432) SacII CCGCgg 19 19 PstI CTGCAg 20 24PvuII CAGctg 20 22 AvaI Cycgrg 21 24 EagI Cggccg 21 22 AatII GACGTc 2222 BspMI ACCTGC 27 33 AccI GTmkac 30 43 StyI Ccwwgg 36 49 AlwNICAGNNNctg 38 44 BsaI GGTCTCNnnnn 38 44 (SEQ ID NO: 433) PpuMI RGgwccy 4346 BsgI GTGCAG 44 54 BseRI NNnnnnnnnnctcctc 48 60 (SEQ ID NO: 434) EciInnnnnnnnntccgcc 52 57 (SEQ ID NO: 435) BstEII Ggtnacc 54 61HC Fr4, 47/79  have one EccO109I RGgnccy 54 86 BpmI ctccag 60 121 AvaIIGgwcc 71 140

TABLE 21  MALIA3, annotated ! MALIA3 9532 bases  !  (SEQ ID NO: 451)      1 aat act act act att act aga att gat gcc acc ttt tca gct cgc gcc !    gene ii continued     49 cca aat gaa aat ata gct aaa cag gtt att gac cat ttg cga aat gta     97 tct aat ggt caa act aaa tct act cgt tcg cag aat tgg gaa tca act    145 gtt aca tgg aat gaa act tcc aga cag cgt act tta gtt gca tat tta    193 aaa cat gtt gag cta cag cac cag att cag caa tta agc tct aag cca    241 tcc gca aaa atg acc tct tat caa aaa gag caa tta aag gta ctc tct    289 aat cct gac ctg ttg gag ttt gct tcc ggt ctg gtt cgc ttt gaa gct    337 cga att aaa acg cga tat ttg aag tct ttc ggg ctt cct ctt aat ctt    385 ttt gat gca atc cgc ttt gct tct gac tat aat agt cag ggt aaa gac    433 ctg att ttt gat tta tgg tca ttc tcg ttt tct gaa ctg ttt aaa gca    481 ttt gag ggg gat tca ATG aat att tat gac gat tcc gca gta ttg gac !          RBS?......      Start gene x, ii continues    529 gct atc cag tct aaa cat ttt act att acc ccc tct ggc aaa act tct    577 ttt gca aaa acc tct cgc tat ttt ggt ttt tat cgt cgt ctg gta aac    625 gag ggt tat gat agt gtt gct ctt act atg cct cgt aat tcc ttt tgg    673 cgt tat gta tct gca tta gtt gaa tgt ggt att cct aaa tct caa ctg    721 atg cat ctt tct acc tat aat aat gtt gtt ccg tta gtt cat ttt att    769 aac gta gat ttt tct tcc caa cgt cct gac tgg tat aat gag cca gtt    817 ctt aaa atc gca TAA  !                      End X & II    832 ggtaattca ca  !  (SEQ ID NO: 623) !        M1             E5                 Q10                 T15    843 ATG att aaa gtt gaa att aaa cca tct caa gcc caa ttt act act cgt !      Start gene V  ! !      S17         S20                 P25                 E30    891 tct ggt gtt tct cgt cag ggc aag cct tat tca ctg aat gag cap ctt !  !              V35                 E40                 V45    939 tgt tac gtt gat ttg ggt aat gaa tat ccg gtt ctt gtc aag att act !  !          D50                 A55                 L60    987 ctt gat gaa ggt cag cca gcc tat gcg cct ggt cTG TAC Acc gtt cgt !                                                   BsrGI... !      L65                 V70                 575                 R80   1035 ctg tcc tct ttc aaa gtt ggt cag ttc ggt tcc ott atg att gac cgt !  !                      P85     K87 end of V   1083 ctg cgc ctc gtt ccg gct aag TAA C  !   1108 ATG gag cag gtc gcg gat ttc gac aca att tat cag gcg atg !      Start gene VII  !   1150 ata caa atc tcc gtt gta ctt tgt ttc gcg ctt ggt ata atc  ! !                        VII and IX overlap. !                        ..... S2  V3  L4  V5    (SEQ ID NO: 624)       S10   1192 gct ggg ggt caa agA TGA gt gtt tta atg tat tct ttc gcc tct ttc gtt !                          End VII  !                        |start IX !      L13     W15                 G20                 T25             E29   1242 tta ggt tgg tgc ctt cgt agt ggc att acg tat ttt acc cgt tta atg gaa !    1293 act tcc tc  ! !        .... stop of IX, IX and VIII overlap by four bases   1301 ATG aaa aag tct tta gtc ctc aaa gcc tct gta gcc gtt gct acc ctc !      Start signal sequence of viii.  !   1349 gtt ccg atg ctg tct ttc gct gct gag ggt gac gat ccc gca aaa gcg !                                  mature VIII --->  1397 acc ttt aac tcc ctg caa gcc tca gcg acc gaa tat atc ggt tat gcg   1445 tgg gcg atg gtt gtt gtt att   1466 gtc ggc gca act atc ggt atc aag ctg ttt aag   1499 aaa ttc acc tcg aaa gca ! 1515  !       ...........  −35  .. !   1517      agc tga taaaccgat aoaattaaag gctccttttg !                      ..... −10   ...  !   1552 gagccttttt ttttGGAGAt ttt ! S.D. underlined  ! !           <------ III signal sequence ---------------------------- ->!            M   K   K   L   L   F   A   I   P   L   V (SEQ ID NO: 452)   1575 caac GTG aaa aaa tta tta ttc gca att cct tta gtt ! 1611  ! !       V   P   F   Y   S   H   S   A   Q   1612 gtt cct ttc tat tct cac aGT acA Cag tCT !                               ApaLI...  !   1642     GTC GTG ACG CAG CCG CCC TCA GTG TCT GGG GCC CCA GGG CAG            AGG GTC ACC ATC TCC TGC ACT GGG AGC AGC TCC AAC ATC GGG GCA !            BstEII...   1729     GGT TAT GAT GTA CAC TGG TAC CAG CAG CTT CCA GGA ACA GCC CCC AAA   1777     CTC CTC ATC TAT GGT AAC AGC AAT CCC CCC TCA GGG GTC CCT GAC CGA   1825     TTC TCT GGC TCC AAG TCT GGC ACC TCA GCC TCC CTG GCC ATC ACT   1870     GGG CTC CAG GCT GAG GAT GAG GCT GAT TAT   1900     TAC TGC CAG TCC TAT GAC AGC AGC CTG ACT   1930     GGC CTT TAT GTC TTC GGA ACT GGG ACC AAG GTC ACC GTC !                                                BstEII...   1969     CTA GGT CAG CCC AAG GCC AAC CCC ACT GTC ACT   2002     CTG TTC CCG CCC TCC TCT GAG GAG CTC CAA GCC AAC AAG GCC ACA CTA   2050     GTG TGT CTG ATC ACT CAC TTC TAC CCD GGA GCT GTG ACA GTG GCC TGG   2098     AAG GCA GAT AGC AGC CCC GTC AAG GCG GGA GTG GAG ACC ACC ACA CCC   2146     TCC AAA CAA ACC AAC AAC AAC TAC CCC CCC ACC ACC TAT CTC ACC CTC   2194     ACG CCT GAG CAG TGG AAG TCC CAC AGA AGC TAC AGC TGC CAG GTC ACG   2242     CAT GAA GGG AGC ACC GTG GAG AAG ACA GTG GCC CCT ACA GAA TGT TCA   2290     TAA TAA ACCG CCTCCACCGG GCGCGCCAAT TCTATTTCAA GGAGACAGTC ATA !                                AscI..... !  (SEQ ID NO: 453) !          PelB signal---------------------------------------------->!           M   K   Y   L   L   P   T   A   A   A   G   L   L   L   L   2343     ATG AAA TAC CTA TTG CCT ACG GCA GCC GCT GGA TTG TTA TTA CTC !  !          16  17  18  19  20  21  22 !          A   A   Q   P   A   M   A   2388    gcG GCC ccg ccG GCC atg gcc  !          sfiI..............!                   NgoMi...(1/2)  !                          NcoI  ! !                                   FR1(DP47/V3 23)---------------!                                   23  24  25  26  27  28  29  30 !                                    E   V   Q   L   L   E   S   G   2409                              gaa|gtt|CAA|TTG|tta|gag|tct|ggt| !                                         | MfeI  |  ! !      --------------FR1-------------------------------------------- !       31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !        G   G   L   V   Q   F   G   G   S   L   R   L   S   C   A   2433 |gac|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct| ! !      ----FR1---------------->|...CDR1................|---FR2------ !       46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !        A   S   G   F   T   F   S   S   Y   A   M   S   W   V   R   2478 |gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|atg|tct|tgg|gtt|cgC| !      | BspEI |                     | BsiWI|                     |BstXI. !  !       -------FRS-------------------------------->|...CDR2......... !       61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !        Q   A   P   G   K   G   L   E   W   V   S   A   I   S   G   2523 |CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct|gct|atc|tct|ggt| !   ...BstXI  ! !     .....CDR2............................................|---FR3--- !       76  77  78  79  80  31  82  83  34  35  86  87  88  39  90 !        S   G   G   S   T   Y   Y   A   D   S   V   K   G   R   F   2568 |tct|ggt|ggc|agt|act|tac|tat|gct|gac|tcc|gtt|aaa|ggt|cgc|ttc|  ! !  !      --------FR3--------------------------------------------------!        91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !        T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M   2613 |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg| !              | XbaI  | ! !      ---FR3----------------------------------------------------->|!       106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !        N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K   2658 |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa| !             |AflII |               | PstI |  ! !      .......CDR3.................|----FR4------------------------- !       121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !        D   Y   E   G   T   G   Y   A   F   D   I   W   G   Q   G   2703 |gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gaC|ATA|TGg|ggt|caa|ggt| !                                             | NdeI |(1/4)  !!      --------------FR4---------->|!       136 137 138 139 140 141 142  !        T   M   V   T   V   S   S   2748 |act|atG|GTC|ACC|gtc|tct|agt  !             | BstEII | ! From BstEII onwards, pV323 is same as pCEB1, except as noted. ! BstEII sites may occur in light chains; not likely to be unique in final ! vector.  ! !                         143 144 145 146 147 148 149 150 151 152 !                          A   S   T   K   G   P   S   V   F   P   2769                    gcc tcc acc aaG GGC CCa tcg GTC TTC ccc !                                       Bsp120I.      BbsI...(2/2) !                                       ApaI....  ! !      153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 !       L   A   P   S   S   K   S   T   S   G   G   T   A   A   L   2799 ctg gca ccC TCC TCc aag agc acc tct ggg ggc aca gcg gcc ctg !                BseRI...(2/2)  ! !        168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 !         G   C   L   V   K   D   Y   F   P   E   P   V   T   V   S   2844   ggc tgc ctg GTC AAG GAC TAC TTC CCc gaA CCG GTg acg gtg tcg !                                              AgeI....  ! !        183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 !         W   N   S   G   A   L   T   S   G   V   H   T   F   P   A   2889   tgg aac t|a GGC GCC ctg ace ago ggc gto cac ace ttc ccg gct !                    KasI...(1/4)  ! !        198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 !         V   L   Q   S   S   G   L   Y   S   L   S   S   V   V   T  2934   gtc cta cag tCt agc GGa ctc tac tcc ctc age ago gta gtg acc !                    (Bsu36I...)(knocked out)  ! !        213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 !         V   P   S   S   S   L   G   T   Q   T   Y   I   C   N   V   2979   gtg ccC tct tct agc tTG Ggc acc cag acc tac atc tgc aac gtg !                 (BstXI..........)N.B. destruction of BstXI & Bpmi sites. !  !        228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 !         N   H   K   P   S   N   T   K   V   D   K   K   V   E   P   3024   aat cac aag ccc agc aac acc aag gtg gac aag aaa gtt gag ccc  ! !        243 244 245 !         K   S   C   A   A   A   H   H   H   H   H   H   S   A   3069   aaa tCt tgt GCG GCC GCt aat cac cac cat cat cac tct gct !                    NotI...... ! !         E   Q   K   L   I   S   E   E   D   L   N   G   A   A   3111   gaa caa aaa ctc atc tca gaa aag gat ctg cat agt gcc gca  !  ! !         D   I   N   D   D   R   M      A   S  G   A   3153   GAT ATC aac gat gat cgt atg   gct AGC ggc gcc!        rEK cleavage site..........   NheI... KasI... !        EcoRV..  ! ! Domain 1 ------------------------------------------------------------!           A   E   T   V   E   S   C   L   A   3183     gct gaa act gtt gaa agt tat tta gca  !  ! !       K   P   H   T   E   I   S   F   3210 aaa ccc cat aca gaa aat tca ttt  ! !       T   N   V   W   K   D   D   K   T   3234 aCT AAC CTC TGG AAA CAC CAC AAA Act  ! !       L   D   R   Y   A   N   Y   E   G   C   L   W   N   A   T   G   V   3261 tta aat cgt tac gct aac tat gag ggt tgt ctg tgG AAT GCt aca ggc gtt !                                                    BsmI     ! !       V   V   C   T   G   D   F   T   Q   C   Y   G   T   W   V   P   I   3312 gta gtt tgt act ggt GAC GAA ACT CAG TGT TAC GGT ACA TGG GTT cct att !  !       G   L   A   I   P   E   N   3363 agg ctt gct atc cct aaa aat  ! ! LI linker ------------------------------------!       E   G   G   G   S   E   G   G   G   S   3384 gag ggt ggt ggc tct gag ggt ggc ggt tct  ! !       E   G   G   G   S   E   G   G   G   T   3414 gag ggt ggc ggt tct gag ggt ggc ggt act  !  ! Domain 2   3444 aaa cct cct gag tac aat gat aca cct att ccg ggc tat act tat atc aac   3495 cct ctc gac ggc act tat ccg cct ggt act gag caa aac ccc gct aat cct   3546 aat cct tct ctt GAG GAG tct cag cct ott aat act ttc atg ttt cag aat !                      BseRI     3597 act agg ttc cga aat agg cag ggg gca tta act gtt tat acg ggc act   3645 gtt act caa ggc act gac ccc gtt aaa act tat tac cag tac act cct   3693 gta tca tca aaa gcc atg tat gac gct tac tgg aac ggt aaa ttC AGA !                                                                AIwNI   3741 GAC TGc gct ttc cat tct ggc ttt act gaa gat cca ttc gtt tgt gac!       AlwNI   3789 tat caa ggc caa tcg tct gac ctg cct caa cct cct gtc aat gct  !   3634 ggc ggc ggc trt !  start L2--------------------------------------------------------------  3846 ggt ggt ggt tct    3858 ggt ggc ggc tct   3870 gag ggt ggt ggc tct gag ggt ggc ggt tct   3900 gag ggt ggc ggc tct gag gga ggc ggt too   3930 aat ggt ggc tct ggt    ! end L2  !  ! Domain 3  (SFQ ID NO: 454) ----------------------------------------------------------------!       S   G   D   F   D   Y   F   K   M   A   N   A   N   K   G   A   3945 tcc ggt gat ttt gat tat gaa aag atg gca aac gct aat aag ggg gct ! !       M   T   E   N   A   D   E   N   A   L   Q   S   D   A   K   G   3993 atg act gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc ! !       K   L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F   4041 aaa ctt gat tct gtc gct act gat tac ggt gct gct atc gat ggt ttc ! !       I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   N   4089 att ggt gaa gtt tcc ggc ctt gct aat ggt cat ggt gct act ggt gat ! !       F   A   G   S   N   S   Q   M   A   Q   V   G   D   G   D   N   4137 ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt gat aat ! !       S   P   L   M   N   N   F   R   Q   Y   I   P   S   L   P   Q   4185 tca cct tta atg aat aat ttc cgt caa tat tta cct tcc ctc cct caa !  ! S V ECR P F V F SAPKPVE   4233 too gtt gaa tgt ego cot ttt gtc ttt ago get ggt aaa oca tat gaa !  t FSIDCDKINLF.R. 4281 ttt tot att aat tgt gac aaa ata aac tta tto cgt  ! End Domain 3  ! ! PVFAFLLYVATFMFVF140 4317 oat pee ttt peg ttt ctt tta tat gtt gee ace ttt atg tat gta ttt ! start transmembrane segment  !  ! STFANIL 4365 tot acg ttt got aao ata ctg  t  ! ANKES 4386 opt aat aag gag tot TAA ! stop ot iii  ! Intracellular anchor.  ! (SEQ ID NO: 455)  ! Mi P2VLL5GIP1,1,101,RFLG15 4404 to ATP coa gtt Ott ttg ggt att cog tta tta ttg opt ttc etc ggt ! Start VI  ! 4451 tte ott ctg gta act ttg tto ggc tat ctg ott act ttt ott aaa aag 4499 ggc tte ggt aag ata got att got att tea ttg ttt ott pot ott att 4547 att ggg ott aao toa att ott gtg ggt tat etc tot gat att age got 4595 caa tta ccc tot gac ttt gtt cap ggt gtt cap tta att oto cog tot 4643 aat pop ott coo tgt ttt tat gtt att oto tot gta aag got got att 4691 tte att ttt gac gtt aaa caa aaa ate gtt tot tat ttg gat tgg gat  ! (SEQ ID NO: 456)  ! Ni A2 V3 F5 LILO G13 4739 aaa TAA t ATP got gtt tat ttt qta act ggc aaa tta ggo tot. gga ! end VI Start gene I  ! ! 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  I KTLVSVPKTOCKTVA 4785 aag aog oto att age gtt ggt aag att cap gat aaa att gta got  ! ! 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43  ! PCKIATNLDLRLQNL 4830 aaa tgc aaa ata gee act net ott gat tta egg ott eaa aac etc  ! ! 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58  ! PQVGRFAKTPRVLKI 4875 cog caa gtc ggg agg ttc get aaa acg cot ego gtt ott aga ata  ! ! 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73  ! PDKPSISDLLAIGAG   4920 ccg gat aag cct tct ata tct gat ttg ctt gct att qgg ogc ggt  ! !       74   75 76  77  73  79  80  81  82  83  84  85  86  37  88 !       N   D   S   Y   D   E   N   K   N   G   L   L   V   L   D   4965 aat gat tcc tac gat gaa aat aaa aac ggc ttg ctt gtt ctc gat  ! !       89  90  91  92  93  94  95  96  97  98  99 100 101 102 103 !       E   C   G   T   W   F   N   T   R   S   W   N   D   K   K   5010 aaa tgc ggt act tgg ttt aat acc cgt tct tgg aat gat aaa gaa  ! !      104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 !       R   Q   P   I   I   D   W   R   L   H   A   R   R   L   G   5055 aga cag ccg att att gat tgg ttt cta cat gct cgt aaa tta gga  ! !      119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 !       W   H   I   I   F   L   V   Q   D   L   S   I   V   D   K   5100 tgg gat att att ttt ctt gtt cag gac tta tct att gtt gat aaa !      134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 !       Q   A   R   S   A   L   A   E   H   V   V   Y   Q   R   R   5145 cag gcg cgt tct gca tta gct gaa cat gtt gtt tat tgt cgt cgt ! !      149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 !       L   D   R   I   T   L   P   F   V   G   T   L   Y   S   L   5190 ctg sac aga att act tta cct ttt gtc ggt act tta tat tct ctt  ! !      164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 !       I   T   H   S   R   M   P   L   P   R   L   H   V   G   V   5235 att act ggc tcg aaa atg cct ctg cct aaa tta cat gtt ggc gtt  ! !      179 180 181 182 183 184 185 186 137 188 189 190 191 192 193 !       V   R   Y   G   D   S   Q   L   S   P   T   V   E   R   W   5280 gtt aaa tat ggc gat tct caa tta agc cct act gtt gag cgt tgg  ! !      194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 !       L   Y   T   H   R   N   L   Y   N   A   Y   H   T   R   Q   5325 ctt tat act ggt aag aat ttg tat aac gca tat gat act aaa cag  ! !      209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 !       A   F   S   S   N   Y   D   S   H   V   Y   S   Y   L   T   5370 gct ttt tct agt aat tat gat tcc ggt gtt tat tct tat tta acg  ! !      224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 !       P   Y   L   S   E   G   R   Y   F   R   P   L   N   L   G   5415 cct tat tta tca cac ggt cgg tat ttc aaa cca tta aat tta ggt  !!      239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 !       Q   R   M   R   L   T   R   I   Y   L   K   K   F   S   R   5460 cag aag atg aaa tta act aaa ata tat ttg aaa aag ttt tct cgc  ! !      254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 !       V   L   C   L   A   I   G   F   A   S   A   F   T   Y   S   5505 gtt ctt tgt ctt gcg att gga ttt gca tca gca ttt aca tat apt  ! !      269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 !       Y   I   T   Q   P   K   P   E   V   R   R   V   V   S   Q   5550 tat ata acc caa cct aag ccg gag gtt aaa aag ata gtc tct cag  ! !      224 225 286 227 222 229 290 251 292 293 254 255 296 297 292 !       T   Y   D   F   D   K   F   T   I   D   S   S   Q   R   L   5595 acc tat gat ttt gat aaa ttc act att gac tct tct cag cgt ctt !      299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 !       N   L   S   Y   R   Y   V   F   K   D   S   K   C   K   I   5640 aat cta agc tat cgc tat gtt ttc aag gat tct aag gga aaa TTA !                                                              PacI  !        314 315 316 317 318 319 320 321 322 323 324 325 326 327 328         I   N   S   D   H   L   Q   K   Q   C   Y   S   L   T   Y   5685 ATT AAt agc gac gat tta cag aaa caa ggt tat tca ctc aca tat !     PacI  ! !      329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 !      i  I   D   L   C   T   V   S   I   K   K   G   N   S   N   E                                                             (SEQ ID NO: 620) !     iv                                                       M1  K   5730   att gat tta tgt act gtt tcc att aaa aaa gat aat tca aAT Gaa !                                                             Start IV !  !         344 345 346 347 348 349 !     i    I   V   K   C   N   .End of I !     iv    L3  L   N5  V   I7  N    F  V10   5775    att gtt aaa tgt aat TAA T TTT GTT  !  IV continued   5800 ttc ttg atg ttt gtt tca tca tct tct ttt gct cag gta att gaa atg   5848 aat aat tcg cct ctg cgc gat ttt gta act tgg tat tca aag caa tca   5896 ggc aaa tcc gtt att att tct ccc gat gta aaa ggt act att act gta   5944 tat tca tct gac gtt aaa cct gaa aat cta cgc aat ttc ttt att tct   5992 gtt tta cgt act aat aat ttt gat atg gtt ggt tca att cct tcc ata   6040 att cag aag tat aat cca aat aat cag gat tat att gat gaa ttg cca   6088 tca ttt gat aat cag gaa tat gat gat cat tcc act cct tct ggt ggt   6136 ttc ttt gtt ccg caa aat gat aat gtt act caa act ttt aaa att aat   6184 aac gtt cgg gca aag gat tta ata cga gtt gtc gaa ttg ttt gta aag   6232 tct aat act tct caa tcc tca aat gta tta tct att gac ggc tct aat   6280 cta tta gtt gtt tTT gca cct aaa gat att tta gat aac ctt cct caa !                       ApaLI removed   6328 ttc ctt tct act gtt gat ttg cca act gac cag ata ttg att gag ggt   6376 ttg ata ttt gag gtt caa caa ggt gat gct tta gat ttt tca ttt gct   6424 gct ggc tct cag cgt ggc act gtt gca ggc ggt gtt aat act gac cgc   6472 ctc acc tct gtt tta tct tct gct aat ggt tcg ttc ggt att ttt cat   6520 ggc gat gtt tta ggg cta tca gtt cgc gca tta aag act aat agc cat   6568 tca aaa ata ttg tct gtg cca cgt att ctt acg ctt tca ggt ccg aag   6616 ggt tct atc tct gtT GGC CAg aat gtc cct ttt att act ggt cgt gtg !                        MscI         6664 act ggt gaa tct gcc aat gta aat act cca ttt cag acg att gag cgt   6712 caa aat gta ggt att tcc atg agc gtt ttt cct gtt gca atg gct ggc   6760 ggt act att gtt ctg gat att acc agc aag gcc gat agt ttg agt tct   6808 tct act cag gca agc gat gtt att act act caa aga agt att gct aca   6856 acg gtt aat ttg cgt gat gga cag act ctt tta ctc ggt ggc ctc act   6904 gat tat aaa aac act tct caa gat tct ggc gta ccg tta ctg tct aaa   6952 atc cct tta atc ggc ctc ctg ttt agc tcc cgc tct gat tcc aac gag   7000 gaa agc acg tta tac gtg ctc gtc aaa gca acc ata gta cgc gcc ctg   7048 TAG cggcgcatt  !      End IV   7060 aagcacggcg ggtgtggtaa ttacgcgcag ogtgaccgct acacttgcca gcgccctagc   7120 gcccgctcct ttcgctttct tcccttcctt tctcgccaca ttcGCCGGCt ttccccgtca !                                                     NgoMI_   7180 agctctaaat cgggggctcc ctttagggtt ccgatttagt actttacggc acctoaaccc   7240 caaaaaactt gatttgggtg atggttCACG TAGTGggcca tcgccctgat agacggtttt !                                  DraIII       7300 tcgccctttG ACGTTGGAGT Ccacgttctt taatagtgga ctcttgttcc aaactggaac!               DrdI              7360 aacactcaac cctatctcgg gctattcttt tgatttataa gggattttgc cgatttcgga   7420 accaccatca aacaggattt tcgcctgctg gggcaaacca gcgtggaccg cttgctgcaa   7480 ctctctcagg gccaggcggt gaagggcaat CAGCTGttgc cCGTCTCact ggtgaaaaga !                                       PvuII.      BsmBI.   7540 aaaaccaccc tGGATCC AAGCTT  !                  BamHi HindIII (½)                    Insert carrying bla gene   7563    gcaggtg gcacttttcg gggaaatgtg ogcggaacee   7600 ctatttgttt atttttctaa atacattcaa atatGTATCC gctcatdaaa caataaccct !                                           BciVI   7660 gataaatgct tcaataatat tgaaaaAGGA AGAgt !                                  RBS.?...  !      Start bla gene   7695 ATG agt att caa cat ttc cgt gtc gcc ctt att ccc ttt ttt gcg gca ttt   7746 tgc ctt cct gtt ttt gct cac cca gaa acg ctg gtg aaa gta aaa gat gct   7797 gaa gat cag ttg ggC gCA CGA Gtg ggt tac atc gaa ctg gat ctc aac agc!                           BssSI... !                       ApaLI removed   7848 ggt aag atc ctt gag agt ttt cgc ccc gaa gaa cgt ttt cca atg atg agc   7899 act ttt aaa gtt ctg cta tgt cat aca cta tta tcc cgt att gac gcc ggg   7950 caa aaG CAA CTC GGT CGc cgg acg cag tat tat cag aat gac ttg gtt gAG !            BcgI                                                       ScaI   8001 TAC Tca cca gtc aca gaa aag cat ctt acg gat ggc atg aca gta aga gaa !      ScaI_  8052 tta tgc agt gct gcc ata acc atg agt gat aac act gcg gcc aac tta ctt   8103 cta aca aCG ATC Gga gga ccg aag aag cta acc gct ttt ttg cac aac atg !               PvuI      8154 ggg gat cat gta act cgc ctt gat cgt tgg gaa ccg gag ctg aat gaa gcc   8205 ata cca aac gac gag cgt gac acc acg ctg cct gta gca atg cca aca acg   8256 tTG CGC Aaa cta tta act ggc gaa cta ctt act cta gct tcc cgg caa caa !       FspI....  !   8307 tta ata gac tgg atg gag gcg gat aaa gtt gca gga cca ctt ctg cgc tcg   8358 GCC ctt ccG GCt ggc tgg ttt att gct gat aaa tct gga gcc ggt gag cgt !      BglI             8409 gGG TCT Cgc ggt atc att gca gca ctg ggg cca gat ggt aag ccc tcc cgt !       BsaI   8460 atc ata gtt atc tac act ACg ggg aGT Cag gca act atg gat gaa cga aat !                            AhdI             8511 aga cag atc gct gag ata ggt gcc tca ctg att aag cat tgg TAA ctgt !                                                              stop   8560 cagaccaagt ttactcatat atactttaga ttgatttaaa acttcatttt taatttaaaa   8620 ggatctaggt gaagatcctt tttgataatc tcatgaccaa aatcccttaa cgtgagtttt   8680 cgttccactg tacgtaagac cccc   8704 AAGCTT GTCGAC tgaa tggcgaa gg cgotttgcct  !      HindIII SalI.. !      (2/2) HincII   8740 ggtttccggc accagaagcg dtgccggaaa dctggctgga gtgcgatctt  !   8790 CCTGAGG  !      Bsu36I_  8797 cogat actgtegtcg tcooctcaaa ctggcagatd   8832 caccidttacg atgcgcccat ctacaccaac dtaacctatc ccattaccidt caatccgccg   8992 t.t.i+32gttr ,ggagaal-r′r′ gF.rgggttgt tartcgr-,-,, atttaatgt tgatgagr..   8952 tdactacagg aaggccagac acgaattatt tttgatggcg ttoctattag ttaaaaaatg   9012 agctgattta acaaaaattt aacgcgaatt ttaacaaaat attaacgttt acaATTTAAA !                                                                Swai...   9072 Tatttgctta tacaatcttc ctgtttttgg gguttttttg attatcaacc GGGGTAcat !                                                             RBS?   9131 ATG att gac atg roe gtt tta cga tta ccg ttc atc gat tct ctt gtt tgc !      Start gene II   9182 tcc aga ctc tca ggc aat gac ctg ata gcc ttt gtA GAT CTc tca aaa ata !                                                    BgiII...   9233 gct ccc ctc tcc ggc atg aat tta tca gct aga acg gtt gaa tat cat ctt   9284 gat ggt gat ttg act gtc tcc ggc ctt tct cac cct ttt gaa tct tta cct   9335 aca cat tac tca ggc att gca ttt aaa ata tat gag ggt tct aaa aat ttt   9386 tat cct tgc gtt gaa ata aag gct tct ccc gca aaa gta tta cag ggt cat   9437 aat gtt ttt ggt aca acc gat tta gct tta tgc tct gag gct tta ttg ctt   9488 aat ttt gct aat tct ttg cct tgc ctg tat gat tta ttg gat gtt ! 9532 ! gene II continues 

TABLE 21B  Sequence of MALIA3, condensed LOCUS MALIA3 9532 CIRCULARORIGIN (SEQ ID NO: 451) 1AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT 61ATAGCTAAAC AGGTTATTGA CCATTTGCGA AATGTATCTA ATGGTCAAAC TAAATCTACT 121CGTTCGCAGA ATTGGGAATC AACTGTTACA TGGAATGAAA CTTCCAGACA CCGTACTTTA 181GTTGCATATT TAAAACATGT TGAGCTACAG CACCAGATTC AGCAATTAAG CTCTAAGCCA 241TCCGCAAAAA TGACCTCTTA TCAAAAGGAG CAATTAAAGG TACTCTCTAA TCCTGACCTG 301TTGGAGTTTG CTTCCGGTCT GGTTCGCTTT GAAGCTCGAA TTAAAACGCG ATATTTGAAG 361TCTTTCGGGC TTCCTCTTAA TCTITTTGAT GCAATCCGCT TTGCTTCTGA CTATAATAGT 421CAGGGTAAAG ACCTGATTTT TGATTTATGG TCATTCTCGT TTTCTGAACT GTTTAAAGCA 481TTTGAGGGGG ATTCAATGAA TATTTATGAC GATTCCGCAG TATTGGACGC TATCCAGTCT 541AAACATTTTA CTATTACCCC CTCTGGCAAA ACTTCTTTTG CAAAAGCCTC TCGCTATTTT 601GGTTTTTATC GTCGTCTGGT AAACGAGGGT TATGATAGTG TTGCTCTTAC TATGCCTCGT 661AATTCCTTTT GGCGTTATGT ATCTGCATTA GTTGAATGTG GTATTCCTAA ATCTCAACTG 721ATGAATCTTT CTACCTGTAA TAATGTTGTT CCGTTAGTTC GTTTTATTAA CGTAGATTTT 781TCTTCCCAAC GTCCTGACTG GTATAATGAG CCAGTTCTTA AAATCGCATA AGGTAATTCA 841CAATGATTAA AGTTGAAATT AAACCATCTC AAGCCCAATT TACTACTCGT TCTGGTGTTT 901CTCGTCAGGG CAAGCCTTAT TCACTGAATG AGCAGCTTTG TTACGTTGAT TTGGGTAATG 961AATATCCGGT TCTTGTCAAG ATTACTCTTG ATGAAGGTCA GCCAGCCTAT GCGCCTGGTC 1021TGTACACCGT TCATCTGTCC TCTTTCAAAG TTGGTCAGTT CGGTTCCCTT ATGATTGACC 1081GTCTGCGCCT CGTTCCGGCT AAGTAACATG GAGCAGGTCG CGGATTTCGA CACAATTTAT 1141CAGGCGATGA TACAAATCTC CGTTGTACTT TGTTTCGCGC TTGGTATAAT CGCTGGGGGT 1201CAAAGATGAG TGTTTTAGTG TATTCTTTCG CCTCTTTCGT TTTAGGIIGG TGCCTTCGTA 1261GTGGCATTAC GTATTTTACC CGTTTAATGG AAACTTCCTC ATGAAAAAGT CTTTAGTCCT 1321CAAAGCCTCT GTAGCCGTTG CTACCCTCGT TCCGATGCTG TCTTTCGCTG CTGAGGGTGA 1381CGATCCCGCA AAAGCGGCCT TTAACTCCCT GCAAGCCTCA GCGACCGAAT ATATCGGTTA 1441TGCGTGGGCG ATGGTTGTTG TCATTGTCGG CGCAACTATC GGTATCAAGC TGTTTAAGAA 1501ATTCACCTCG AAAGCAAGCT GATAAACCGA TACAATTAAA GGCTCCTTTT GGAGCCTTTT 1561TTTTTGGAGA TTTTCAACGT GAAAAAATTA TTATTCGCAA TTCCTTTAGT TGTTCCTTTC 1621TATTCTCACA GTGCACAGTC TGTCGTGACG CAGCCGCCCT CAGTGTCTGG GGCCCCAGGG 1681CAGAGGGTCA CCATCTCCTG CACTGGGAGC AGCTCCAACA TCGGGGCAGG TTATGATGTA 1741CACTGGTACC AGCAGCTTCC AGGAACAGCC CCCAAACTCC TCATCTATGG TAACAGCAAT 1801CGGCCCTCAG GGGTCCCTGA CCGATTCTCT GGCTCCAAGT CTGGCACCTC AGCCTCCCTG 1861GCCATCACTG GGCTCCAGGC TGAGGATGAG GCTGATTATT ACTGCCAGTC CTATGACAGC 1921AGCCTGAGTG GCCTTTATGT CTTCGGAACT GGGACCAAGG TCACCGTCCT AGGTCAGCCC 1981AAGGCCAACC CCACTGTCAC TCTGTTCCCG CCCTCCTCTG AGGAGCTCCA AGCCAACAAG 2041GCCACACTAG TGTGTCTGAT CAGTGACTTC TACCCGGGAG CTGTGACAGT GGCCTGGAAG 2101GCAGATAGCA GCCCCGTCAA GGCGGGAGTG GAGACCACCA CACCCTCCAA ACAAAGCAAC 2161AACAAGTACG CGGCCAGCAG CTATCTGAGC CTGACGCCTG AGCAGTGGAA GTCCCACAGA 2221AGCTACAGCT GCCAGGTCAC GCATGAAGGG AGCACCGTGG AGAAGACAGT GGCCCCTACA 2281GAATGTTCAT AATAAACCGC CTCCACCGGG CGCGCCAATT CTATTTCAAG GAGACAGTCA 2341TAATGAAATA CCTATTGCCT ACGGCAGCCG CTGGATTGTT ATTACTCGCG GCCCAGCCGG 2401CCATGGCCGA AGTTCAATTG TTAGAGTCTG GTGGCGGTCT TGTTCAGCCT GGTGGTTCTT 2461TACGTCTTTC TTGCGCTGCT TCCGGATTCA CTTTCTCTTC GTACGCTATG TCTTGGGTTC 2521GCCAAGCTCC TGGTAAAGGT TTGGAGTGGG TTTCTGCTAT CTCTGGTTCT GGTGGCAGTA 2581CTTACTATGC TGACTCCGTT AAAGGTCGCT TCACTATCTC TAGAGACAAC TCTAAGAATA 2641CTCTCTACTT GCAGATGAAC AGCTTAAGGG CTGAGGACAC TGCAGTCTAC TATTGCGCTA 2701AAGACTATGA AGGTACTGGT TATGCTTTCG ACATATGGGG TCAAGGTACT ATGGTCACCG 2761TCTCTAGTGC CTCCACCAAG GGCCCATCGG TCTTCCOCCT GGCACCCTCC TCCAAGAGCA 2921CCTCTGGGGG CACAGCGGCC CTGGGCTGCC TGGTCAAGGA CTACTTCCCC GAACCGGTGA 2881CGGTGTCGTG GAACTCAGGC GCCCTGACCA GCGGCGTCCA CACCTTCCCG GCTGTCCTAC 2941AGTCTAGCGG ACTCTACTCC CTCAGCAGCG TAGTGACCGT GCCCTCTTCT AGCTTGGGCA 3001CCCAGACCTA CATCTGCAAC GTGAATCACA AGCCCAGCAA CACCAAGGTG GACAAGAAAG 3061TTGAGCCCAA ATCTTGTGCG GCCGCTCATC ACCACCATCA TCACTCTGCT GAACAAAAAC 3121TCATCTCAGA AGAGGATCTG AATGGTGCCG CAGATATCAL CGATGATCGT ATGGCTGGCG 3181CCGCTGAAAC TGTTGAAAGT TGTITAGCAA AACCCCATAC AGAAAATTCA TTTACTAACG 3241TCTGGAAAGA CGACAAAACT TTAGATCGTT ACGCTAACTA TGAGGGTTGT CTGTGGAATG 3301CTACAGGCGT TGTAGTTTGT ACTGGTGACG AAACTCAGTG TTACGGTACA TGGGTTCCTA 3361TTGGGCTTGC TATCCCTGAA AATGAGGGTG GTGGCTCTGA GGGTGGCGGT TCTGAGGGTG 3421GCGGTTCTGA GGGTGGCGGT ACTAAACCTC CTGAGTACGG TGATACACCT ATTCCGGGCT 3481ATACTTATAT CAACCCTCTC GACGGCACTT ATCCGCCTGG TACTGAGCAA AACCCCGCTA 3541ATCCTAATCC TTCTCTTGAG GAGTCTCAGC CTCTTAATAC TTTCATGTTT CAGAATAATA 3601GGTTCCGAAA TAGGCAGGGG GCATTAACTG TTTATACGGG CACTGTTACT CAAGGCACTG 3661ACCCCGTTAA AACTTATTAC CAGTACACTC CTGTATCATC AAAAGCCATG TATGACGCTT 3721ACTGGAACGG TAAATTCAGA GACTGCGCTT TCCATTCTGG CTTTAATGAA GATCCATTCG 3781TTTGTGAATA TCAAGGCCAA TCGTCTGACC TGCCTCAACC TCCTGTCAAT GCTGGCGGCG 3841GCTCTGGTGG TGGTTCTGGT GGCGGCTCTG AGGGTGGTGG CTCTGAGGGT GGCGGTTCTG 3901AGGGTGGCGG CTCTGAGGGA GGCGGTTCCG GTGGTGGCTC TGGTTCCGGT GATTTTGATT 3961ATGAAAAGAT GGCAAACGCT AATAAGGGGG CTATGACCGA AAATGCCGAT GAAAACGCGC 4021TACAGTCTGA CGCTAAAGGC AAACTTGATT CTGTCGCTAC TGATTACGGT GCTGCTATCG 4081ATGGTTTCAT TGGTGACGTT TCCGGCCTTG CTAATGGTAA TGGTGCTACT GGTGATTTTG 4141CTGGCTCTAA TTCCCAAATG GCTCAAGTCG GTGACGGTGA TAATTCACCT TTAATGAATA 4201ATTTCCGTCA ATATTTACCT TCCCTCCCTC AATCGGTTGA ATGTCGCCCT TTTGTCTTTA 4251GCGCTGGTAA ACCATATGAA TTTTCTATTG ATTGTGACAA AATAAACTTA TTCCGTGGTG 4321TCTTTGCGTT TCTTTTATAT GTTGCCACCT TTATGTATGT ATTTTCTACG TTTGCTAACA 4381TACTGCGTAA TAAGGAGTCT TAATCATGCC AGTTCTTTTG GGTATTCCGT TATTATTGCG 4441TTTCCTCGGT TTCCTTCTGG TAACTTTGTT CGGCTATCTG CTTACTTTTC TTAAAAAGGG 4501CTTCGGTAAG ATAGCTATTG CTATTTCATT GTTTCTTGCT CTTATTATTG GGCTTAACTC 4561AATTCTTGTG GGTTATCTCT CTGATATTAG CGCTCAATTA CCCTCTGACT TTGTTCAGGG 4621TGTTCAGTTA ATTCTCCCGT CTAATGCGCT TCCCTGTTTT TATGTTATTC TCTCTGTAAA 4681GGCTGCTATT TTCATTTTTG ACGTTAAACA AAAAATCGTT TCTTATTTGG ATTGGGATAA 4741ATAATATGGC TGTTTATTTT GTAACTGGCA AATTAGGCTC TGGAAAGACG CTCGTTAGCG 4801TTGGTAAGAT TCAGGATAAA ATTGTAGCTG GGTGCAAAAT AGCAACTAAT CTTGATTTAA 4861GGCTTCAAAA CCTCCCGCAA GTCGGGAGGT TCGCTAAAAC GCCTCGCGTT CTTAGAATAC 4921CGGATAAGCC TTCTATATCT GATTTGCTTG CTATTGGGCG CGGTAATGAT TCCTACGATG 4981AAAATAAAAA CGGCTTGCTT GTTCTCGATG AGTGCGGTAC TTGGTTTAAT ACCCGTTCTT 5041GGAATGATAA GGAAAGACAG CCGATTATTG ATTGGTTTCT ACATGCTCGT AAATTAGGAT 5101GGGATATTAT TTTTCTTGTT CAGGACTTAT CTATTGTTGA TAAACAGGCG CGTTCTGCAT 5161TAGCTGAACA TGTTGTTTAT TGTCGTCGTC TGGACAGAAT TACTTTACCT TTTGTCGGTA 5221CTTTATATTC TCTTATTACT GGCTCGAALA TGCCTCTGCC TAAATTACAT GTTGGCGTTG 5281TTAAATATGG CGATTCTCAA TTAAGCCCTA CTGTTGAGCG TTGGCTTTAT ACTGGTAAGA 5341ATTTGTATAA CGCATATGAT ACTAAACAGG CTTTTTCTAG TAATTATGAT TCCGGTGTTT 5401ATTCTTATTT AACGCCTTAT TTATCACACG GTCGGTATTT CAAACCATTA AATTTAGGTC 5461AGAAGATGAA ATTAACTALA ATATATTTGA AAAAGTTTTC TCGCGTTCTT TGTCTTGCGA 5521TTGGATTTGC ATCAGCATTT ACATATAGTT ATATAACCCA ACCTAAGCCG GAGGTTAAAA 5581AGGTAGTCTC TCAGACCTAT GATTTTGATA AATTCACTAT TGACTCTTCT CAGCGTCTTA 5641ATCTAAGCTA TCGCTATGTT TTCAAGGATT CTAAGGGAAA ATTAATTAAT AGCGACGATT 5701TACAGAAGCA AGGTTATTCA CTCACATATA TTGATTTATG TACTGTTTCC ATTAAAAAAG 5751GTAATTCAAA TGAAATTGTT AAATGIAATT AATTTTGTTT TCTTGATGTT TGTTTCATCA 5821TCTTCTTTTG CTCAGGTAAT TGAAATGAAT AATTCGCCTC TGCGCGATTT TGTAACTTGG 5881TATTCAAAGC AATCAGGCGA ATCCGTTATT GTTTCTCCCG ATGTALLAGG TACTGTTACT 5941GTATATTCAT CTGACGTTAA ACCTGALLAT CTACGCAATT TCTTTATTTC TGTTTTACGT 6001GCTAATAATT TTGATATGGT TGGTTCAATT CCTTCCATAA TTCAGAAGTA TAATCCAAAC 6051AATCAGGATT ATATTGATGA ATTGCCATCA TCTGATAATC AGGAATATGA TGATAATTCC 6121CCTCCTTCTC CTCCTTTCTT TCTTCCCCAA AATCATAATC TTACTCAAAC TTTTAAAATT 6181AATAACGTTC GGGCAAAGGA TTTAATACGA GTTGTCGAAT TGTTTGTAAA GTCTAATACT 6241TCTAAATCCT CAAATGTATT ATCTATTGAC GGCTCTAATC TATTAGTTGT TTCTGCACCT 6301AAAGATATTT TAGATAACCT TCCTCAATTC CTTTCTACTG TTGATTTGCC AACTGACCAG 6351ATATTGATTG AGGGTTTGAT ATTTGAGGTT CAGCAAGGTG ATGCTTTAGA TTTTTCATTT 6421CCTCCTGOCT CTCAGCGTCC CACTOTTGCA CGCOGTOTTA ATACTGACCC CCTCACCTCT 6481GTTTTATCTT CTGCTGGTGG TTCGTTCGGT ATTTTTAATG GCGATGTTTT AGGGCTATCA 5541GTTCGCGCAT TAAAGACTAA TAGCCATTCA AAAATATTGT CTGTGCCACG TATTCTTACG 6601CTTTCAGGTC AGAAGGGTTC TATCTCTGTT GGCCAGAATG TCCCTTTTAT TACTGGTCGT 6661GTGACTGGTG AATCTGCCAA TGTAAATAAT CCATTTCAGA CGATTGAGCG TCAAAATGTA 5721CCTATTTCCA TCACCCTTTT TCCTCTTCCA ATCCCTCOCC CTAATATTCT TCTCCATATT 6731ACCAGCAAGG CCGATAGTTT GAGTTCTTCT ACTCAGGCAA GTGATGTTAT TACTAATCAA 6841AGAAGTATTG CTACAACGGT TAATTTGCGT GATGGACAGA CTCTTTTACT CGGTGGCCTC 6901ACTGATTATA AAAACACTTC TCAAGATTCT GGCGTACCGT TCCTGTCTAA AATCCCTTTA 6961ATCGGCCTCC TGTTTAGCTC CCGCTCTGAT TCCAACGAGG AAAGCACGTT ATACGTGCTC 7021GTCAAAGCAA CCATAGTACG CGCCCTGTAG CGGCGCATTA AGCGCGGCGG GTGTGGTGGT 7081TACGCGCAGC GTGACCGCTA CACTTGCCAG CGCCCTAGCG CCCGCTCCTT TCGCTTTCTT 7141CCCTTCCTTT CTCGCCACGT TCGCCGGCTT TCCCCGTCAA GCTCTAAATC GGGGGCTCCC 7201TTTAGGGTTC CGATTTAGTG CTTTACGGCA CCTCGACCCC AAAAAACTTG ATTTGGGTGA 7261TGGTTCACGT AGTGGGCCAT CGCCCTGATA GACGGTTTTT CGCCCTTTGA CGTTGGAGTC 7321CACGTTCTTT AATAGTGGAC TCTTGTTCCA AACTGGAACA ACACTCAACC CTATCTCGGG 7381CTATTCTTTT GATTTATAAG GGATTTTGCC GATTTCGGAA CCACCATCAA ACAGGATTTT 7441CGCCTGCTGG GGCAAACCAG CGTGGACCGC TTGCTGCAAC TCTCTCAGGG CCAGGCGGTG 7501AAGGGCAATC AGCTGTTGCC CGTCTCACTG GTGAAAAGAA AAACCACCCT GGATCCAAGC 7561TTGCAGGTGG CACTTTTCGG GGAAATGTGC GCGGAACCCC TATTTGTTTA TTTTTCTAAA 7621TACATTCAAA TATGTATCCG CTCATGAGAC AATAACCCTG ATAAATGCTT CAATAATATT 7681GAAAAAGGAA GAGTATGAGT ATTCAACATT TCCGTGTCGC CCTTATTCCC TTTTTTGCGG I74iCATTTTGCCT TCCTGTTTTT GCTCACCCAG AAACGCTGGT GAAAGTAAAA GATGCTGAAG 7301ATCAGTTGGG CGCACGAGTG GGTTACATCG AACTGGATCT CAACAGCGGT AAGATCCTTG 7861AGAGTTTTCG CCCCGAAGAA CGTTTTCCAA TGATGAGCAC TTTTAAAGTT CTGCTATGTC 7921ATACACTATT ATCCCGTATT GACGCCGGGC AAGAGCAACT CGGTCGCCGG GCGCGGTATT 7981CTCAGAATGA CTTGGTTGAG TACTCACCAG TCACAGAAAA GCATCTTACG GATGGCATGA 8041CAGTAAGAGA ATTATGCAGT GCTGCCATAA CCATGAGTGA TAACACTOCC GCCAACTTAC 8101TTCTGACAAC GATCGGAGGA CCGAAGGAGC TAACCGCTTT TTTGCACAAC ATGGGGGATC 8161ATGTAACTCG CCTTGATCGT TGGGAACCGG AGCTGAATGA AGCCATACCA AACGACGAGC 8221GTGACACCAC GATGCCTGTA GCAATGCCAA CAACGTTGCG CAAACTATTA ACTGGCGAAC 8281TACTTACTCT AGCTTCCCGG CAACAATTAA TAGACTGGAT GGAGGCGGAT AAAGTTGCAG 8341GACCACTTCT GCGCTCGGCC CTTCCGGCTG GCTGGTTTAT TGCTGATAAA TCTGGAGCCG 8401GTGAGCGTGG GTCTCGCGGT ATCATTGCAG CACTGGGGCC AGATGGTAAG CCCTCCCGTA 8461TCGTAGTTAT CTACACGACG GGGAGTCAGG CAACTATGGA TGAACGAAAT AGACAGATCG 8521CTGAGATAGG TGCCTCACTG ATTAAGCATT GGTAACTGTC AGACCAAGTT TACTCATATA 8581TACTTTAGAT TGATTTAAAA CTTCATTTTT AATTTAAAAG GATCTAGGTG AAGATCCTTT 8641TTGATAATCT CATGACCAAA ATCCCTTAAC GTGAGTTTTC GTTCCACTGT ACGTAAGACC 8701CCCAAGCTTG TCGACTGAAT GGCGAATGGC GCTTTGCCTG GTTTCCGGCA CCAGAAGCGG 8761TGCCGGAAAG CTGGCTGGAG TGCGATCTTC CTGAGGCCGA TACTGTCGTC GTCCCCTCAA 8821ACTGGCAGAT GCACGGTTAC GATGCGCCCA TCTACACCAA CGTAACCTAT CCCATTACGG 8881TCAATCCGCC GTTTGTTCCC ACGGAGAATC CGACGGGTTG TTACTCGCTC ACATTTAATG 8941TTGATGAAAG CTGGCTACAG GAAGGCCAGA CGCGAATTAT TTTTGATGGC GTTCCTATTG 9001GTTAAAAAAT GAGCTGATTT AACAAAAATT TAACGCGAAT TTTAACAAAA TATTAACGTT 9061TACAATTTAA ATATTTGCTT ATACAATCTT CCTGTTTTTG GGGCTTTTCT GATTATCAAC 9121CGGGGTACAT ATGATTGACA TGCTAGTTTT ACGATTACCG TTCATCGATT CTCTTGTTTG 9181CTCCAGACTC TCAGGCAATG ACCTGATAGC CTTTGTAGAT CTCTCAAAAA TAGCTACCCT 9241CTCCGGCATG AATTTATCAG CTAGAACGGT TGAATATCAT ATTGATGGTG ATTTGACTGT 9301CTCCGGCCTT TCTCACCCTT TTGAATCTTT ACCTACACAT TACTCAGGCA TTGCATTTAA 9361AATATATGAG GGTTCTAAAA ATTTTTATCC TTGCGTTGAA ATAAAGGCTT CTCCCGCAAA 9421AGTATTACAG GGTCATAATG TTTTTGGTAC AACCGATTTA GCTTTATGCT CTGAGGCTTT 9431ATTGCTTAAT TTTGCTAATT CTTTGCCTTG CCTGTATGAT TTATTGGATG TT

TABLE 22  Primers used in RACE amplification: Heavy chainHuCμ-FOR (1^(st) PCR)5′-TGG AAG AGG CAC GTT CTT TTC TTT-3′ (SEQ ID NO: 457)HuCμ-Nested (2^(nd) PCR)5′ CTT TTC TTT GTT GCC GTT GGG GTG-3′ (SEQ ID NO: 458) Kappa light chainHuCkFor (1^(st) PCP)5′-ACA CTC TCC CCT GTT GAA GCT CTT-3′ (SEQ ID NO: 459)HuCkForAscI (2^(nd) PCR)5′-ACC GCC TCC ACC GGG SOC GCC TTA TTA ACA CTC TCCCCE GEE GAA OCT CTT-3′ (SEQ ID NO: 460) Lambda light chainHuClambdaFor (1^(st) PC(K) HuCL2-FOR5′-TGA ACA TTC TGT ASS GGC CAC TG-3′ (SEQ ID NO: 461) HuCL7-FOR5′-AGA GCA TTC TGC AGG GGC CAC TG-3′ (SEQ ID NO: 462)HuClambdaForAscI (2^(nd) PC(K) HuCL2-FOR-ASC5′-ACC GCC TCC ACC GGG CGC GCC TTA TTA TGA ACA TTCTGT AGG GGC CAC TG-3′ (SEQ ID NO: 463) HuCL7-FOR-ASC5′-ACC GCC TCC ACC GGG CGC GCC ETA TTA AGA GCA TTCTGC AGG GGC CAC TG-3′ (SEQ ID NO: 464)GeneRAcer 5′ Primers provided with the kit (invitrogen) 5′A 1^(st) PCR(SEQ ID NO: 465) 5′ CGACTGGAGCACGAGGACACTGA 3′ 5′NA 2^(nd) pCR5′GGACACTGACATGGACTGAAGGAGTA-3′ (SEQ ID NO: 466)

TABLE 23 ONs used in Capture of kappa light chains using CJ method and BsmAIREdapter (6) ON_20SK15012 gggAggATggAgAcTcggTc (SEQ ID NO: 467)ON_20SK15L12 gggAAgATggAgAcTgggTc (SEQ ID NO: 468) ON_20SK15A17gggAgAgTggAgAcTcAgTc (SEQ ID NO: 469) ON_20SK15A27gggTgccTggAgAcTgcgTc (SEQ ID NO: 470) ON-20SK15A11gggTggcTggAgAcTgcgTc (SEQ ID NO: 471) ON:20SK15B3gggAgTcTggAgAcTgggTc (residues 1-20 of SEQ ID NO: 477) Bridges (6)kapbri1012gggAggATggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg (SEQ ID NO: 472)kapbri1L12gggAAgATggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg (SEQ ID NO: 473)5apbrilA17gggAgAgTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg (SEQ ID NO: 474)kapbrilA27gggTgccTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg (SEQ ID NO: 475)kaphrilA11gggTggcTggAgArTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg (SEQ ID NO: 476)kapbrilB3gggAgTcTggAgAcTgggTcATcTggATgTcTTgTgoAcTgTgAcAgAgg (SEQ ID NO: 477)Extender (5′ biotinylated) kapext1bioccTcTgTcAcAgTgcAcAAgAcATccAgATgAcccAgTcTcc (SEQ ID NO: 478) PrimerskaPCRt1 ccTcTgTcAcAgTgcAcAAgAc (SEQ ID NO: 479) kapfor5′-aca ctc tcc cct gtt gaa gct ctt-3′ (SEQ ID NO: 480) All ONs arewritten 5′ to 3′.

TABLE 24  PCR program for amplification of kappa DNA 95° C.   5 minutes95° C.  15 seconds 65° C.  30 seconds 72° C.   1 minute 72° C.  7 minutes  4° C. hold Reagents (100 ul reaction): Template  50 np10K turbo PCR buffer   1x turbo Pfu  40 dNTPs 200 uM each kaPCRt1 300 nMkapfor 300 nM

TABLE 25  h3401-h2 captured Via CJ with BsmAI(Nucleotide sequence is SEQ ID NO: 481; amino acid sequence is SEQ ID NO: 482)!  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !  S   A   Q   D   I   Q   M   T   Q   S   P   A   T   L   S    aGT GCA C aa gac atc cag atg acc cag tct cca gcc acc ctg tct !  ApaLI...                                 a gcc acc ! L25, L6, L20, L2, L16, A11! Extender..................................Bridge... ! 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  V   S   P   G   E   R   A   T   L   S   C   R   A   S   Q   gtg tct cca ggg gaa agg gcc acc ctc tcc tgc agg gcc agt cag ! 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !  S   V   S   N   N   L   A   W   Y   Q   Q   K   P   G   Q   agt gtt agt aac aac tta gcc tgg tac cag cag aaa cct ggc cag! 46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !  V   P   R   L   2   I   Y   G   A   S   T   R   A   T   D   gtt ccc agg ctc ctc atc tat ggt gca tcc acc agg gcc act gat ! 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !  I   P   A   R   F   S   G   S   G   S   G   T   D   F   T   atc cca gcc agg ttc agt ggc agt ggg tct ggg aca gac ttc act ! 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !  L   T   I   S   R   L   E   P   E   D   F   A   V   Y   Y   ctc acc atc agc aga ctg gag cct gaa gat ttt gca gtg tat tac ! 91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !  C   C   R   Y   G   S   S   P   G   W   T   F   G   Q   G   tat tag cgg tat ggt agc tca ccg ggg tgg acg ttc ggc caa ggg ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  T   K   V   E   I   K   R   T   V   A   A   P   S   V   F   acc aag gtg aaa atc aaa cga act gtg gct gca cca tct gtc ttc ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  I   F   P   P   S   D   E   Q   L   K   S   G   T   A   S   atc ttc ccg cca tct gat gag cag ttg aaa tct gga act gcc tct ! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  V   V   C   L   2   N   N   F   Y   P   R   E   A   K   V   gtt gtg tgc ctg ctg aat aac ttc tat ccc aga gag gcc aaa gta ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  Q   W   K   V   D   N   A   L   Q   S   G   N   S   Q   E    cag tgg aag gtg gat aac gcc ctc caa tcg ggt aac tcc cag gag ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  S   V   T   E   Q   D   S   K   D   S   T   Y   S   L   S   agt gtc aca gag cag gac agc aag gac agc acc tac agc ctc agc ! 131 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  S   T   L   T   L   S   K   A   D   Y   F   K   H   K   V   agc acc ctg acg ctg agc aaa gca gac tac gag aaa cac aaa gtc! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  Y   A   C   E   V   T   H   Q   G   L   S   S   P   V   T   tac gcc tgc gaa gtc acc cat cag ggc ctg agc tcg cct gtc aca ! 211 212 213 214 215 216 217 218 219 220 221 222 223 !  K   S   F   N   K   G   E   C   K   G   S   F   A   aag agc ttc aac aaa gga gag tgt aag ggc gaa ttc gc.....

TABLE 26 h3401-d8 KAPPA captured with CJ and EsmAI(Nucleotide sequence is SEQ ID NO: 484; amino acid sequence is SEQ ID NO: 485)!  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !  S   A   Q   D   I   Q   M   T   Q   S   P   A   T   L   S    aGT GCA C aa gac atc cag atg acc cag tct cct gcc acc ctg tct !  ApaLI...Extender......................... a gcc acc ! L25, L6, L20, L2, L16, A11                                            A GCC ACC CTG TCT ! L2 (SEQ ID NO: 483)!  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  V   S   P   G   E   R   A   T   L   S   C   R   A   S   Q   gtg tct cca ggt gas aga gcc acc ctc tcc tgc agg gcc agt cag ! GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !     L2 !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !  N   L   L   S   N   L   A   W   Y   Q   Q   K   P   G   Q   aat ctt ctc agc aac tta gcc tgg tac cag cag aaa cct ggc cag !  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !  A   P   R   L   L   I   F   G   A   S   T   G   A   I   G   gct ccc agg ctc ctc atc tat act gct tcc acc ggg gcc att ggt !  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !  I   P   A   R   F   S   G   S   G   S   G   T   E   F   T   atc cca acc agg ttc agt ggc cct ggg tct ggg aca gag ttc act !  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !  L   T   I   S   S   L   Q   S   E   D   F   A   V   F   F   ctc acc atc agc agc ctg cag tct gaa gat ttt gca gtg tat ttc !  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !  C   Q   Q   Y   G   T   S   P   P   T   F   G   G   G   T   tgt cag cag tat ggt acc tca ccg ccc act ttc ggc gga ggg acc ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  K   V   E   I   K   R   T   V   A   A   P   S   V   F   I   aag gtg gag atc aaa cga act gtg gct gca cca tct gtc ttc atc ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  F   P   P   S   D   E   Q   L   K   S   G   T   A   S   V   ttc ccg cca tct gat gag cag ttg aaa tct gga act gcc tct gtt ! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  V   C   P   L   N   N   F   Y   P   R   E   A   K   V   Q   gtg tgc ccg ctg sat aac ttc tat ccc aga gag gcc aaa gta cag ! 151 152 153 154 155 156 157 153 159 160 161 162 163 164 165 !  W   K   V   D   N   A   L   Q   S   G   N   S   Q   E   S   tgg aag gtg gat aac gcc ctc caa tcg ggt aac tcc cag gag aqt ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  V   T   E   Q   D   N   K   D   Q   T   Y   S   L   S   S  gtc aca gag cag gac aac aag gac agc acc tac agc ctc agc agc ! 181 182 133 184 185 186 187 188 189 190 191 192 193 194 195 !  T   L   T   L   S   K   V   D   Y   E   K   H   E   V   Y   acc ctg acg ccg agc aaa gta gac tac gag aaa cac gaa gtc tac ! 196 197 193 199 200 201 202 203 204 205 206 207 200 209 210 !  A   C   E   V   T   H   Q   G   S   S   S   P   V   T   H   gct tgc gaa gtc act cat tag ggc ctt agc tcg ccc gtc acg aag ! 211 212 213 214 215 216 217 218 219 220 221 222 223 !  S   F   N   R   G   F   C   K   K   E   F   V   agc tcc aac agg gga gag tgt aag aaa gaa ttc gtt t 

TABLE 27 V3-23 VP framework with variegated rodeos shown! (Nucleotide sequence is SEQ ID NO: 486; amino acid sequence is SEQ ID NO: 487)!                                    17  18  19  20  21  22 !                                     A   Q   P   A   M   A                    5′- ctg tct gaa cG GCC cag ccG  GCC atg gcc    29                    3′-gac aga ctt gc cgg gtc ggc cgg tac cgg!                     Scab.........SfiI............!                                         NgoMI... !                                                NcoI....  ! !                                    FR1(DP47/V3-23)--------------- !                                    23  24  25  26  27  28  29  30 !                                     E   V   Q   L   L   E   S   C                                      gaa|gtt|CAA|TTG|tta|gag|tct|ggt|   53 !                                    ctt|caa|gtt|aac|aat|ctc|aga|cca|!                                           | MfeI  |  !!        --------------FR1-------------------------------------------- !         31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !          G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A          |ggc|ggt|ctt|gtt| cag | cct | ggt | ggt | tct | tta|cgt|ctt|tct|tgc|gct|  98 !        |ccg|cca|gaa|caa|gtc|gga|cca|cca|aga|aat|gca|gaa|aga|acg|cga| ! !        Sites to be varied--->       ***     ***     *** !        ----FR1---------------->|...CDR1----------------|---FR2------ !         46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !          A   S   G   F   T   F   S   S   Y   A   M   S   W   V   R           | gct | TCC | GGA | ttc |a ct | ttc | tct|tCG|TAC|Gct|atg|tct|tgg | gtt | cgC |  143 !        |cga|agg|cct|aag|tga|aag|aga|agc|atg|cga|tac|aga|acc|caa|gcg|  !            | BspET | BsWI| |BstXI| !!                              Sites to be varies---> ***     *** ***!         -------FR2-------------------------------->|...CDR2......... !         61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !          Q   A   P   G   K   G   L   E   W   V   S   A   I   S   G           | CAa | gct | ccT | GG t|aaa| ggt | ttg | gag | tgg | gtt |tct |gct|atc|tct|ggt| 188 !        |gtt|cga|gga|cca|ttt|cca|aac|ctc|acc|caa|aga|cga|tag|aga|cca|  !    ...BstXI          | !                     ***     *** !       .....CDR2............................................|---FR3--- !         76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !          S   G   G   S   T   Y   Y   A   D   S   V   K   G   R   F          |tct|ggt|ggc|agt|act|tac|ta t | gct | gac | tcc | gtt | aaa |gg t|cgc|ttc| 233 !        |aga|cca|ccg|tca|tga|atg|ata|cga|ctg|agg|caa|ttt|cca|gcg|aag| ! !        --------FR3-------------------------------------------------- !          91  92  83  94  95  96  97  88  90 100 101 102 103 104 105 !          T   I   S   R   D   N   D   K   N   T   L   Y   L   Q   M          |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttc|cag|atg| 278 !        |tga|tag|aga|tct|ctg|ttg|aga|ttc|tta|tga|gag|atg|aac|gtc|tac|!                | XbaI  | ! !        ---FR3----------------------------------------------------->|!         106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !          N   S   L   R   A   D   D   T   A   V   Y   Y   C   A   K          |aac|a gC | TTA | AGg | gct | gag | gac | aCT |GCA|Gtc|tac|tat|tgc|gct|aaa| 323 !        |ttg|tcg|aat|tcc|cga|ctc|ctg|tga|cgt|cag|atg|ata|acg|aga|ttt| !               |AflII |               | PstI |  !!        .......CDR3.................|----FR4------------------------- !         121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !          D   Y   E   C   T   G   Y   A   F   D   I   W   G   Q   G          |gac|tat|gaa|ggt|act|ggt|tat| gct | ttc | gaC | ATA | TGg | ggt| c aa|ggt| 368 !        |ctc|ata|ctt|cca|tga|cca|ata|cga|aag|ctg|tat|acc|cca|gtt|cca| !                                               | NdeI | ! !       --------------FR4---------->| !        136 137 138 139 140 141 142 !         T   M   V   T   V   S   S         |act|atG|GTC|ACC|gtc|tct|agt- 339 !       |tga|tac|cag|tgg|cag|aga|tca-  !              | BstEII | !                         143 144 145 146 147 148 149 150 151 152 !                          A   S   T   K   G   P   S   V   F   P                           gcc tcc acc aaG GGC CCa tcg GTC TTC ccc-3′   419 !                         cgg agg t gg ttc ccg ggt agc cag aag ggg -5′ !                                       Bsp120I.      BBsI...(2/2) !                                       ApaI.... (SFPRMET)  5′-ctg tct gaa cG GCC cag ccG-3′ (SEQ ID NO: 488) (TOPFR1A)  5′-ctg tct gaa cG GCC cag ccG GCC atg gcc-               gaa|gtt|CAA|TTG|tta|gac|tct|ggt|-             |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta-3′ (SEQ ID NO: 489) (BOTFR1B)              3′-caa|gtc|gga|cca|cca|aga|aat|gca|gaa|aga|acg|cga|-              |cga|agg|cct|aag|tga|aag-5′ ! bottom strand (SEQ ID NO: 490) (BOTFR2)   3′-acc|caa|gcg|-              |gtt|cga|gga|cca|ttt|cca|aac|ctc|acc|caa|aga|-5′ ! bottom strand  (SEQ ID NO: 491)  (BOTFR3)   3′-  a|cga|ctg|agg|caa|ttt|cca|gcg|aag|-              |tga|tag|aga|tct|ctg|ttg|aga|ttc|tta|tga|gag|atg|aac|gtc|tac|-          |ttg|tcg|aat|tcc|cga|ctc|ctg|tga-5′ (SEQ ID NO: 492) (F06)       5′-gC|TTA|AGg|gct|gag|gac!aCT|GCA|Gtc|tac|tat|tgc|cct|aaa|-         |gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gaC|ATA|TGg|ggt|c-3′ (SEQ ID NO: 493)(BOTFR4)   3′-cga|aag|ctg|tat|acc|cca|gtt|cca|-              |tga|tac|cag|tgg|cag|aga|tca-                  cgg agg tgg ttc ccg ggt agC cag aag ggg-5′ ! bottom strand (SEQ ID NO: 494) (BOTPRCPRIM)           3′-gg ttc ccg ggt agC cag aag ggg-5′ (SEQ ID NO: 495) !  ! CDR1 diversity  ! (ON-vgCl)   5′-|gct|TCC|GGA|ttc|act|ttc|tct|<1>|TAC|<1>|atg|<1>| - !                                       CDR1...................6859                |tga|gtt|cgC|CAa|gct|ccT|GG-3′  (SEQ ID NO: 496)  !!<1> stands for an equimolar mix of {ADEFGHIKLMNPQRSTVWY}; no C !                                  (this is not a sequence)  ! ! CDR2 diversity  ! (ON-vgC2)   5′-ggt|ttg|gag|tgg|gtt|tct|<2>|atc|<2>|<3>|-!                                      CDP2                 |tct|ggt|ggc|<1>|act|<1>|tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 497) !               CDP2................................................! <1> is an equimolar mixture of {ADEFGHIKLMKPQRSTVWY}; no C ! <2> is an equimolar mixture of {YRWVGS}; no ACDEFRIKLMNPQT! <3> is an equimoiar mixture of {PS}; no ACDEFGHIKLMNQRTVWY 

TABLE 28 Stutter used in VH (SEQ ID NO: 498)  1 TCCGGAGCTT CAGATCTGTT TGCCTTTTTG TGGGGTGGTG CAGATCGCGT TACGGAGATC 61 GACCGACTGC TTGAGCAAAA GCCACGCTTA ACTGCTGATC AGGCATGGGA TGTTATTCGC121 CAAACCAGTC GTCAGGATCT TAACCTGAGG CTTTTTTTAC CTACTCTGCA AGCAGCGACA181 TCTGGTTTGA CACAGAGCGA TCCGCGTCGT CAGTTGGTAG AAACATTAAC ACGTTGGGAT241 GGCATCAATT TGCTTAATGA TGATGGTAAA ACCTGGCAGC AGCCAGGCTC TGCCATCCTG301 AACGTTTGGC TGACCAGTAT GTTGAAGCGT ACCGTAGTGG CTGCCGTACC TATGCCATTT361 GATAAGTGGT ACAGCGCCAG TGGCTACGAA ACAACCCAGG ACGGCCCAAC TGGTTCGCTG421 AATATAAGTG TTGGAGCAAA AATTTTGTAT GAGGCGGTGC AGGGAGACAA ATCACCAATC481 CCACAGGCGG TTGATCTGTT TGCTGGGAAA CCACAGCAGG AGGTTGTGTT GGCTGCGCTG541 GAAGATACCT GGGAGACTCT TTCCAAACGC TATGGCAATA ATGTGAGTAA CTGGAAAACA601 CCTGCAATGG CCTTAACGTT CCGGGCAAAT AATTTCTTTG GTGTACCGCA GGCCGCAGCG661 GAAGAAACGC GTCATCAGGC GGAGTATCAA AACCGTGGAA CAGAAAACGA TATGATTGTT721 TTCTCACCAA CGACAAGCGA TCGTCCTGTG CTTGCCTGGG ATGTGGTCGC ACCCGGTCAG781 AGTGGGTTTA TTGCTCCCGA TGGAACAGTT GATAAGCACT ATGAAGATCA GCTGAAAATG841 TACGAAAATT TTGGCCGTAA GTCGCTCTGG TTAACGAAGC AGGATGTGGA GGCGCATAAG901 GAGTCGTCTA GA 

TABLE 29 DNA seguence of bCES5 ! pCES5 6680 bases = pC-804 with stuffers in CDR1-2 and CDR3 2000.12.13 ! ! Ngene = 6680 ! Useful REs (cut MAnoLI fewer than 3 times) 2000.06.05  !! Non-cutters  !Acc651 Ggtacc     AfeI AGCgct          AvrII Cctagg !BsaBI GATNNnnatc  BsiWI Cgtacg         BsmFI Nnnnnnnnnnnnnnngtccc (SEQ ID NO: 499)               (SEQ ID NO: 500) !BsrGI Tgtaca      BstAPI GCANNNNntgc   BstBI TTcgaa              (SEQ ID NO: 501) !BstZ17I GTAtac    BtrI CACgtg          Ecl136I GAGctc !EcoRV GATatc      FseI GGCCGGcc        KpnI GGTACc !MscI TGGcca       NruI TCGcga          NsiI ATGCAt !PacI TTAATtaa     PMeI GTTTaaac        PmlI CACgtg !PpuMI RGgwccy     PshAI GACNNnngtc     SacI GAGCTc                   (SEQ ID NO: 502) !SacII CCGCgg      SbfI CCTGCAgg        SexAI Accwggt !SgfI GCGATcgc     SnaBI TACgta         SpeI Actagt !SphI GCATGc       Sse8387I CCTGCAgg    StuI AGGcct !SwaI ATTTaaat     XmaI Cccggg  ! ! cutters ! Enzymes that cut more than 3 times.  !AlwNI CAGNNNctg            5 !BsgI ctgcac                4  !BsrFI Rccggy               5 !EarI CTCTTCNnnn            4  (SEQ ID NO: 625) !FauI nNNNNNNGCGGG         10  ! (SEQ ID NO: 503) ! Enzymes that cut from 1 to 3 times.  ! !EcoO109I RGgnccy           3      7    2636 4208 !BssSI Ctcgtg               1     22 !-″- Cacgag                 1   1703!BspHI Tcatga               3     43     148 1156 !AatII GACGTc               1     65 !BciVI GTATCCNNNNNN         2    140    1667     (SEQ ID NO: 504) !Eco57I CTGAAG              1    301 !-″- cttcag                 2   1349 !AvaI Cycgrg                3    319    2347 6137 !BsiHKAI GWGCWc             3    401    2321 4245 !HgiAI GWGCWc               3    401    2321 4245 !BcgI gcannnnnntcg          1    461     (SEQ. ID NO: 505)!ScaI AGTact                1    505 !Pvul CGATcy                3    616    3598 5926 !FspI TGCgca                2    763    5946 !BglI GCCNNNNnggc           3    864    2771 5952     (SEQ ID NO: 506) !BgmI CTGGAG                1    898 !-″- ctccag                 1   4413 !BsaI GGTCTCNnnnn           1    916     (SEQ ID NO: 507) !AhdI GACNNNnngtc           1    983  (SEQ ID NO:: 508) !Eam1105I GACNNNnngtc       1    983     (SEQ ID NO: 509) !DrdI GACNNNNnngtc          3   1768    6197 6579     (SEQ ID NO: 510) !SapI gaagagc               1   1998 !PvuII CAGctg               3   2054    3689 5896 !Pf1MI CCANNNNntgg          3   2233    3943 3991     (SEQ ID NO: 511) !HindIII Aagctt             1   2235 !ApaLI Gtgcca               1   2321 !BspMI Nnnnnnnnngcaggt      1   2328     (SEQ ID NO: 512) !-″- ACCTGCNNNNn            2   3460     (SEQ ID NO: 513) !PStI CTGAg                 1   2335 !AccI GTmkac                2   2341    2611 !HincII GTXrac              2   2341    3730 !SalI Gtagac                1   2341 !TliI Ctcgag                1   2347 !XhoI Ctcgag                1   2347 !BbsI gtcttc                2   2383    4219 !B1PI Gctnagc               1   2580 !EspI Gctnagc               1   2580 ! SgrAI CRccggyg            1   2648 !AgeI Accggt                2   2649    4302 !AacI GGcgcgcc              1   2689 !BssHII Gcgcgc              1   2690 !SfiI GGCCNNNNnggcc         1   2770     (SEQ ID NO: 514) !NaeI GCCggc                2   2776    6349 !NgoMIV Gccggc              2   2776    6349 !BtgI Ccrygg                3   2781    3553 5712 !DsaI Ccrygg                3   2781    3553 5712 !NcoI Ccatgg                1   2781 !StyI Ccwwgg                3   2781    4205 4472 !MfeI Caattg                1   2795 !BspEI Tccgga               1   2861 !BglII Agatct               1   2872 !BclI Tgatca                1   2956 !Bsu36I CCtnagg             3   3004    4143 4373 !XcmI CCANNNNNnnnntgg       1   3225     (SEQ ID NO: 515) !MluI Acgcgt                1   3527 !HpaI GTTaac                1   3730 !XbaI Tctaga                1   3767  ! !AflII Cttaag               1   3811 !BsmI NGcattc               1   3821 !-″- GAATGCN                1   4695 !RsrII CGgwccg              1   3827 !NheI Gctagc                1   4166 !BstEII Ggtnacc             1   4182 !BsmBI CGTCTCNnnnn          2   4188    6625     (SEQ ID NO: 516) !-″- Nnnnnngagacg           1   6673     (SEQ ID NO: 517)!ApaI GGGCCc                1   4209 !BanII GGCYc                3   4209    4492 6319 !Bsp120I Gggccc             1   4209 !PspOMI Gggccc              1   4209 !BseRI NNnnnnnnnnctcctc     1   4226     (SEQ ID NO: 518) !-″- GAGGAGNNNNNNNNNN       1   4957     (SEQ ID NO: 519) !EcoNI CCTNNnnnagg          1   4278     (SEQ ID NO: 520) !PflEI GACNnngtc            1   4308 !Tth111I GACNnngtc          1   4308 !KasI Ggcgcc                2   4327    5967 !BstXI CCANNNNNntgg         1   4415     (SEQ ID NO: 521) !NotI GCggccgc              1   4507 !EagI Cggccg                1   4508 !BamHI Ggatcc               1   5169 !BspDI ATcgat               1   5476 !NdeI CAtatg                1   5672 !EcoRI Gaattc               1   5806 !PsiI TTAtaa                1   6118 !DraIII CACNNNgtg           1   6243 !BsaAI YACgtr               1   6246 !------------------------------------------------------------------------(Nucleotide sequence is SEQ ID NO: 522; amino acid sequence is SEQ ID NO: 523, respectively)      1     gacqaaaggg aCTCGTGata cgcctatttt tataggttaa tgtcatgata ataatggttt !                      BssSI.(1/2)     61     cttaGACGTC aggtggcact tttcggggaa atgtgcgcgg aacccotatt tgtttatttt 1              ASCII.    121     tctaaataca ttcaaatatG TATCCgctca tgagacaata accctgataa atgcttcaat !                              BciVI..(1 of 2)    181     aatattgaaa aaggaagagt ! Base #  201 to 1061 = ApR gene from pUC119 with some RE sites removed !!            1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !          fM   S   I   Q   N   E   R   V   A   L   I   P   E   E   A    201     atg agt att caa cat ttc opt gtc gcc ctt att ccc ttt Ltt gcg ! !           16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !           A   F   C   L   P   V   F   A   H   P   E   T   L   V   K     246     gca ttt tgc ctt cct gtt ttt gct cac cca gas acg ctg gtg aaa! !           31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !           V   K   D   A   E   D   Q   L   G   A   R   V   G   Y   I   291     gta aaa gat gct gaa gat cag ttg ggt gcc cga gtg ggt tac atc !!           46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !           E   L   D   L   N   S   G   K   I   L   E   S   F   R   P    336     gaa ctg gat ctc aac agc ggt aag atc cct gag agt ttt cgc ccc ! !           61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !           K   E   R   F   P   M   M   S   T   F   K   V   S   S   C    381     gaa gaa cgt ttt cca atg atg agc act ttt aaa gtt ctg cta tgt ! !           76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !           G   A   V   L   S   K   I   D   A   G   Q   F   Q   S   G    426     ggc gcg gta tta tcc cgt att gac gcc ggg caa gaG CAa ctc ggT !                                                       BcgI.............! !           91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !           R   R   I   H   Y   S   Q   N   D   L   V   E   Y   S   P    471     CGc cgc ata cac tat tat cag cat gac ttg gtt gAG TAC Tca cca !..BcgI...... !!          106 107 508 109 110 111 112 113 114 115 116 117 118 119 120 !           V   T   E   K   H   L   T   D   G   M   T   V   R   E   L    516     gtc aca gaa aag cat ctt acg gat ggc atg aca gta aga gaa tta !!          121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !           C   S   A   A   I   T   M   S   D   N   T   A   A   N   L    561     tgc agt gct gcc ata acc atg agt gat aac act gcg gcc aac tta !!          136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !           L   L   T   T   I   G   G   P   K   E   L   T   A   F   L    606     ctt ctg aca aCG ATC Gga gga ccg aag gag cta acc gct ttt ttg !                       PvuI.... (1/2)  !!          151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !           H   N   M   G   D   H   V   T   R   L   D   R   W   E   P    651     cac aac atg ggg gat cat gta act cgc ctt gat cgt tgg gaa ccg !!          166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !           E   L   N   F   A   I   P   N   D   E   R   D   T   T   M    696     gag ctg aat gaa gcc ata cca aac gac gag cgt gac acc acg atg !!          181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !           P   V   A   M   A   T   T   L   R   K   L   L   T   G   E    741     cct gta GCA ATG gca aca acg tTG CGC Aaa cta tta act ggc gaa !                  BsrDI..(1/2)         FspI.... (1/2)  !!          196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !           L   L   T   L   A   S   R   Q   Q   L   I   D   W   M   E    786     cta ctt act cta gct tcc cgg caa caa tta ata gac tgg atg gag ! !          211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !           A   D   K   V   A   G   P   L   L   R   S   A   L   P   A    831     gcg gat aaa gtt gca gga cca ctt ctg cgc tcg gcc ctt ccg gct ! !          226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !           G   W   F   I   A   D   K   S   G   A   G   E   R   G   S    876     ggc tgg ttt att gct gat aaa tCT GGA Gcc ggt gag cgt gGG TCT !                                       BpmI....(1/2)           BsaI.... !            241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 !           R   G   I   I   A   A   L   G   P   D   G   K   P   S   R    921     Cgc ggt atC ATT GCa gca ctg gag cca gat ggt aag ccc tcc cat ! BsaI......         BsrDI...(2/2)  !           256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 !           I   V   V   I   Y   T   T   G   S   Q   A   T   M   D   E    966     atc gta gtt atc tac acG ACg ggg aGT Cag gca act atg gat gaa !                                AhdT...........  ! !          271 272 272 274 275 276 277 278 279 280 281 282 083 284 285 !           R   N   R   Q   I   A   E   I   G   A   S   L   I   K   H   1011     cga at aga cag atc gct gag ata ggt gcc tca ctg att aag cat  !!          286 287  !           W   .    1056     tgg taa   2062                                                  ctgtcagac caagtttact   1081     catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga   1141     tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt   1201     cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct   1261     gctgcttgca aacaaaaaaa ccaccgctac cagaggtggt ttgtttgccg gatcaagagc   1321     taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgtcc   1381     ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc  1441     tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg   1501     ggttggactc aagacgatag ttaccggata aggcgcagcg gtcggggtga acggggggtt   1561     cgtgcataca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg   1621     agcattgaga aagcgccacg cttcccgaag ggagaaaggc ggacagGTAT CCggtaagcg !                                                            BiVI.. (2 of 2)   1881     gcagggtcgg aacaggagag cgCACGAGgg agcttccagg gggaaacgcc tggtatcttt !                                  BssSI.(2/2)   1741     atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag   1801     gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt   1861     gctggcctct tgctcACATG Ttctttcctg cgttatcccc tgattctgtg gataaccgta !                          PciI...   1921     ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt   1981     cagtgagcga ggaagcgGAA GAGCgcccaa tacgcaaacc gcctctcccc gcgcgttggc!                            SapI....      2041     cgattcatta atgCAGCTGg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca!                        PvuII.(1/3)  2101     acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc!                 ..−35..         Plac                    ..−10.  2161     cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacaCAGGA AACAGCTATG      !                                                           M13Rev_seq_primer  2221     ACcatgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac!                       PtlMI.......  !                         Hinda3. ! signal::linker::CLight  ! !           1   2   3   4   5   8   7   8   9  10  11  12  13  14  15 !          fM   K   K   L   L   F   A   I   P   L   V   V   P   F   Y  (Amino acid sequence is SEO ID NO: 524)  2289     gtg aaa aaa tta tta ttc gca att cct tta gtt gtt cct ttc tat !                            Linker.............................. End of FR4 !          18  17  18  19      20  21  22  23  24  25  28  27  28  29  30 !          S   H   S   A       Q   V   Q   L   Q   V   D   L   E   I   K  2314     tCt oac aGT GCA    Cag gtc caa CTG CAG GTC GAC CTC GAG atc aaa !                   ApaLI......           PstI...         XhoI... !                                           BspMI... !                                                 SalI... !                                                 AccI...(1/2) !                                                 HincII.(1/2)  ! ! Vlight domains could be cloned in as ApaLI-XhoI fragments.! VL-CL(kappa) segments can be cloned in as ApaLI-AscI fragments <--------! !           Ckappa----------------------------------------------------!           31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !           R   G   T   V   A   A   P   S   V   F   I   F   P   P   S   2359     cgt gga act gtg gct gca cca tct GTC TTC atc ttc ccg cca tct!                                          BbsI...(1/2)  ! !           46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !           D   E   Q   L   K   S   G   T   A   S   V   V   C   L   L   2404     gat gag cag ttg aaa tct gga act gcc tct gtt gtg tgc ctg ctg! !           61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !           N   N   F   Y   P   R   E   A   K   V   Q   W   K   V   D   2449     aat aac ttc tat ccc aga gag gcc aaa gta cag tgg aag gtg gat! !           76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !           N   A   L   Q   S   G   N   S   Q   E   S   V   T   E   Q   2494     aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc aca gag cag! !           91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !           D   S   K   D   S   T   Y   S   L   S   S   T   L   P   L   2539     gac agc aag gac agc acc tac agc ctc agc agc acc ctg acG CTG!                                                                EspI... ! !          106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !           S   K   A   D   Y   E   K   H   K   V   Y   A   C   E   V   2584     AGC aaa gca gac tac gag aaa cac aaa GTC TAC gcc tgc gaa gtc!  ...EspI....                                 AccI...(2/2)  ! !          121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !           T   H   Q   G   L   S   S   P   V   T   K   S   F   N   R   2629     acc cat cag ggc ctg agt tcA CCG GTg aca aag agc ttc aac agg !                                    AgeI....(1/2) !          136 137 138 139 140  !           G   E   C   .   .   2674     gga gag tgt taa taa   GG CGCGCCaatt !                                AscI..... !                                 BssHII.   2701     ctatttcaag gagacagtca ta  ! ! PelB::3-23(stuffed)::CH1::III fusion gene  ! !          1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !         M   K   Y   L   L   P   T   A   A   A   G   L   L   L   L  (Amino acid sequence is SEQ ID NO: 525)  2723   atg aaa tac cta ttg cct acg gca gcc gct gga ttg tta tta ctc  ! !-------------------------------------------- ! !       16  17  18  19  20  21  22  !       A   A   Q   P   A   M   A   2768 gcG GCC cag ccG GCC atg gcc  !        SfiI.............!                NgoMIV..(1/2)  !                       NcoI....  ! !                                   FR1(DP47/V3-23)--------------- !                                   23  24  25  26  27  28  29  30 !                                    E   V   Q   L   L   E   S   G   2789                              gaa|gtt|CAA|TTG|tta|gag|tct|ggt| !                                          | MfeI  |  !       !       ---------------FR1-------------------------------------------!        31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !         G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A   2813  |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct| !  !       ----FR1-----  !        46  47  48  !         A   S   G   2858  |gct|TCC|GGA|  !           | BspEI |  !  !          Stuffer for CDR1, FR2, and CDR2--------------------------------->!          Thre are no stop codons in this stuffer.   2867                                                 gcttcAGATC Tgtttgcctt !                                                           BglII..   2887     tttgtggggt ggtgcagatc gcgttacgga gatcgaccga ctgcttgagc aaaagccacg   2947     cttaactgcT GATCAggcat gggatgttat tcgccaaacc agtcgtcagg atcttaacct !                   BclI..   3007     gaggcttttt ttacctactc tgcaagcagc gacatctggt ttgacacaga gcgatccgcg   3067     tcgtcagttg gtagaaacat taacacgttg ggatggcatc aatttgctta atgatgatgg   3127     taaaacctgg cagcagccag gctctgccat cctgaacgtt tggctgacca gtatgttgaa   3187     gcgtaccgta gtggctgccg tacctatgCC Atttgataag TGGtacagcg ccagtggcta!                                        XcmI.............  3247     cgaaacaacc caggacggcc caactggttc gctgaatata agtgttggag caaaaatttt   3307     gtatgaggcg gtgcagggag acaaatcacc aatcccacag gcggttgatc tgtttgctgg   3367     gaaaccacag caggaggttg tgttggctgc gctggaagat acctgggaga ctctttccaa   3427     acgctatggc aataatgtga gtaactggaa aacacctgca atggccttaa cgttccgggc   3487     aaataatttc tttggtgtac cgcaggccgc agcggaagaa ACGCGTcatc aggcggacta !                                                      MluI..   3547     tcaaaaccgt ggaacagaaa acgatatgat tgttttctca ccaacgacaa gcgatcgtcc  3607     tgtgcttgcc tgggatgtgg tcgcacccgg tcagagtggg tttattgctc ccgatggaac   3667     agttgataag cactatgaag atcagctgaa aatgtacgaa aattttggcc gtaagtcgct!                                  PvuII.   3727     ctgGTTAACg aagcaggatg tggaggcgca taaggagtcg!             HpaI..  !             HincII(2/2) !!       --------FR3--------------------------------------------------!                 4   5   6   7   8   9   10  11  12  13  14  15  16 !                 93  94  95  96  97  98  99 100 101 102 103 104 105 !                 S   R   D   N   S   K   N   T   L   Y   L   Q   M      (Amino acid SEQ ID NO: 526)  3767          |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|!               | XbaI  | ! !       ---FR3----------------------------------------------------->|!         17  18  19  20  !  !        106 107 108 109 !         N   S   L   s    l   s   i   r   s   g  3806  |acc|agC|TTA|AG t ctg agc att CGG TCC G  !              |aflII |!  !              q   h   s   p   t   .  3834     gg caa cat tct cca aac tga   ccagacga cacaaacggc   3872     ttacgctaaa tcccgcgcat gggatggtaa agaggtggcg tctttgctgg cctggactca   3932     tcagatgaag gccaaaaatt ggcaggagtg gacacagcag gcagcgaaac aagcactgac   3992     catcaactgg tactatgctg atgtaaacgg caatattggt tatgttcata ctggtgctta   4052     tccagatcgt caatcaggcc atgatccgcg attacccgtt cctggtacgg gaaaatggga  4112     ctggaaaggg ctattgcctt ttgaaatgaa ccctaaggtg tataaccccc ag  4164           aa GCTAGC ctgcggcttc  !                   NheI..  !   4182     G|GTC|ACC|                                      gtc tca agc!         | BstEII | !         (Amino acid sequence is SEQ ID NO: 527) !          136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !           A   S   T   K   G   P   S   V   F   P   L   A   P   S   S   4198     gcc tcc acc aag ggc cca tcg gtc ttc ccc ctg gca ccc tcc tcc ! !          151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !           K   S   T   S   G   G   T   A   A   L   G   C   S   V   K   4243     aag agc acc tct ggg ggc aca gcg gcc ctg ggc tgc ctg gtc aag ! !          166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !           D   Y   F   P   E   P   V   T   V   S   W   N   S   G   A   4288     gac tac ttc ccc gaa ccg gtg acg gtg tcg tgg aac tca ggc gcc ! !          181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !           L   T   S   G   V   H   T   F   P   A   V   L   Q   S   S   4333     ctg acc agc ggc gtc cac acc ttc ccg gct gtc cta cag tcc tca ! !          196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !           G   L   Y   S   L   S   S   V   V   T   V   P   S   S   S  4378     gga ctc tac tcc ctc agc agc gta gtg acc gtg ccc tcc agc agc! !          211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !           L   G   T   Q   T   Y   I   C   N   V   N   H   K   P   S  4423     ttg ggc acc cag acc tac atc tgc aac gtg aat cac aag ccc agc !  !          226 227 228 229 230 231 232 233 234 235 236 237 238 !           N   T   K   V   D   K   K   V   E   P   K   S   C  4468     aac acc aag gtg gac aaG AAA GTT GAG CCC AAA TCT TGT!                                ON-TQHCforw......................  ! !                                Poly His linker !                    139 140 141 142 143 144 145 146 147 148 149 150 !                     A   A   A   H   H   H   H   H   H   G   A   A   4507               GCG GCC GCa cat cat cat cac cat cac ggg gcc gca!                    NotI......  !                     EagI....  !!        151 152 153 154 155 156 157 158 159 160 161 162 163 264 165 !         E   Q   K   L   I   S   E   E   D   L   N   G   A   A   .   4543   gaa caa aaa ctc atc tca gaa gag gat ctg aat ggg gcc gca tag ! !        Mature III------------------------------------------------>... !        166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !         T   V   E   S   C   L   A   K   P   H   T   E   N   S   F   4588   act gtt gaa agt tgt tta gca aaa cct cat aca gaa aat tca ttt  !!        181 182 183 184 185 186 137 188 189 190 191 192 193 194 195 !         T   N   V   W   K   D   D   K   T   L   D   R   Y   A   N   4633   act aac gtc tgg aaa gac gac aaa act tta gat cgt tac gct aac !!        196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !         Y   E   G   C   L   W   N   A   T   G   V   V   V   C   T   4678   tat gag ggc tgt ctg tgG AAT GCt aca ggc gtt gtg gtt tgt act !                              BsmI....  ! !        211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !         G   D   E   T   Q   C   Y   G   T   W   V   P   I   G   L   4723   ggt qac gaa act cag tgt tac ggt aca tgq qtt cct att ggg ctt  !!        226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !         A   I   P   E   N   E   G   G   G   S   E   C   G   G   S   4768   gct atc cct gaa cat gag ggt ggt ggc tct gag ggt ggc ggt tct  !!        241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 !         E   G   G   G   S   E   G   G   G   T   A   P   P   E   Y   4813   gag ggt ggc ggt tct gag ggt ggc ggt act aaa cct cct gag tac  ! !        256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 !         G   D   T   P   I   P   G   Y   T   Y   I   N   P   L   D   4858   ggt gat aca cct att ccg ggc tat act tat atc aac cct ctc gac ! !        271 272 273 274 275 276 277 278 279 280 291 282 283 284 285!         G   T   Y   P   P   G   T   E   Q   N   P   A   N   P   N   4903   ggc act tat ccg cct ggt act gag caa aac ccc gct aat cct aat  !!        286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 !         P   S   L   E   E   S   Q   P   L   N   T   F   M   F   Q   4948   cct tct ctt GAG GAG tct cag cct ctt act act ttc atg ttt cag !                   EseRI..(2/2)  !!        301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 !         N   N   R   F   R   N   R   Q   G   A   L   T   V   Y   T   4993   aat aat agg ttc cga aat agg cag ggt gca tta act gtt tat acg !!        316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 !         G   T   V   T   Q   G   T   D   P   V   K   T   Y   Y   Q   5038   ggc act gtt act caa ggc act gac ccc gtt aaa act tat tac cag !!        331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 !         Y   T   P   V   S   S   K   A   M   Y   D   A   Y   W   N   5083   tac act cct gta tca tca aaa gcc atg tat gac gct tac tgg aac !        346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 !         G   K   F   R   D   C   A   F   H   S   G   F   N   E   D   5128   ggt aaa ttc aga gac tgc gct ttc cat tct ggc ttt aat gaG GAT !                                                               BamHT... !        361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 !         P   F   V   C   E   Y   Q   G   Q   S   S   D   L   P   Q   5173   CCa ttc gtt tgt gaa tat caa ggc caa tcg tct gAC CTG Cct caa !  BamHI...                                            BspMI...(2/2)  !!        376 377 378 379 380 381 382 383 384 385 386 387 389 289 390 !         P   P   V   N   A   G   G   G   S   G   G   G   S   G   G    5218   cct cct gtc aat gct ggc ggc ggc tct ggt ggt ggt tct ggt ggc !!        391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 !         G   S   E   G   G   G   S   E   G   G   G   S   E   G   G   5263   ggc tct gag ggt ggc ggc tct gag ggt ggc ggt tct gag ggt ggc !!        406 407 408 409 410 411 412 423 414 415 416 417 418 419 420 !         G   S   E   G   G   G   S   G   G   G   S   G   S   G   D   5308   ggc tct gag ggt ggc ggt tcc ggt ggc ggc tcc ggt tcc ggt gat  !!        421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 !         F   D   Y   E   K   M   A   N   A   N   K   G   A   M   T   5353   ttt gat tat gaa aaa atg gca aac gct aat aag ggg gct atg acc  !!        436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 !         E   N   A   D   E   N   A   L   Q   S   D   A   K   G   K   5398   gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc aaa  !!        451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 !         L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F   5443   ctt gat tcc gtc gct act gat tac ggt gct gct ATC GAT ggt ttc !                                                    BspDi..  !!        466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 !         I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   5488   att ggt gac gtt tcc ggc ctt gct aat ggt aat ggt gct act ggt ! !        481 482 483 484 485 486 487 488 489 490 492 492 403 494 495 !         D   F   A   G   S   N   S   N   M   A   Q   V   G   D   G   5533   gat ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt ! !        496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 !         D   N   S   P   L   M   N   N   F   R   Q   Y   L   P   S  5578   gat aat tca cct tta atg aat aat ttc cgt caa tat tta cct tct ! !        511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 !         L   P   Q   S   V   E   C   R   P   Y   V   F   G   A   G  5623   ttg cct cag tcg gtt gaa tgt cgc cct tat gtc ttt ggc gct ggt  !!        526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 !         K   P   Y   E   F   S   I   D   C   D   K   T   N   L   F  5668   aaa cCA TAT Gaa ttt tct att gat tgt gac aaa ata aac tta ttc!             NdeI....  !!        541 542 543 544 545 546 547 548 549 550 551 552 553 554 555!         R   G   V   F   A   F   L   L   Y   V   A   T   F   M   Y   5713   cgt ggt gtc ttt gcg ttt ctt tta tat gtt gcc acc ttt atg tat ! !        556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 !         V   F   S   T   F   A   N   I   L   R   N   K   E   S   .   5758   gta ttt tcg acg ttt gct aac ata ctg cgt aat aag gag tct taa ! !        571  !         .   5803   taa GAATTC !            EcoRI.   5812      actggccgt cgttttacaa cgtcgtgact gggaaaaccc tggcgttacc caacttaatc  5871     gccttgcagc acatccccct ttcgccagct ggcgtaatag cgaagaggcc cgcacCGATC!                                                                      PvuI..   5931     Gcccttccca acagtTGCGC Agcctgaatg gcgaatGGCG CCtgatgcgg tattttctcc! ...PvuI... (3/3)         FspI... (2/2)          KasI...(2/2)   5991     ttacgcatct gtgcggtatt tcacaccgca tataaattgt aaacgttaat attttgttaa   6051     aattcgcgtt aaatttttgt taaatcagct cattttttaa ccaataggcc gaaatcggca   6111     aaatcccTTA TAAatcaaaa gaatagcccg agatagggtt gagtgttgtt ccagtttgga !                 PsiI...   6171     acaagagtcc actattaaag aacgtggact ccaacgtcaa agggcgaaaa accgtctatc   6231     agggcgatgg ccCACtacGT Gaaccatcac ccaaatcaag ttttttgggg tcgaggtgcc !                       DraIII....   6291 gtaaagcact aaatcggaac cctaaaggga gcccccgatt tagagcttga cggggaaaGC !                                                                     NgoMIV..   6351     CGGCgaacgt ggcgagaaag gaagggaaga aagcgaaagg agcgggcgct agggcgctgg !     ..NgoMIV.(2/2)   6411     caagtgtagc ggtcacgctg cgcgtaacca ccacacccgc cgcgcttaat gcgccgctac   6471     agggcgcgta ctatggttgc tttgacgggt gcagtctcag tacaatctgc tctgatgccg   6531     catagttaag ccagccccga cacccgccaa cacccgctga cgcgccctga cgggcttgtc   6591     tgctcccggc atccgcttac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga   6651     ggttttcacc gtcatcaccg aaacgcgcga 

TABLE 30 Oliaonucleotides used to clone CDR1/2 diversityAll sequences are 5′ to 3′. 1) oN_cD1Bsp, 30 bases (SEQ ID NO: 558)  A  c  c  T  c  A  c  T  g  g  c  T  T  c  c  a  g  A  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18  T  T  c  A  c  T  T  T  c  T  c  T 19 20 21 22 23 24 25 26 27 28 29 30 2) ON_Br12, 42 bases (SEQ ID NO: 529)  A  g  A  A  A  c  c  c  A  c  T  c  c  A  A  A  c  c  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18  T  T  T  A  c  c  A  g  g  A  g  c  T  T  g  g  c  g 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36  A  A  c  c  c  A  37 38 39 40 41 42 3) ON_CD2Xba, 51 bases (SEQ ID NO: 53))  g  g  A  A  g  g  c  A  a  T  g  A  T  c  T  A  g  A  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18  g  A  T  A  g  T  g  A  A  g  c  g  A  c  c  T  T  T 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 A  A  c  g  g  A  a  T  c  A  g  c  A  T  A 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 4) ON_BotXba, 23 bases (SEQ ID NO: 531)  g  g  A  A  g  g  c  A  g  T  g  A  T  c  T  A  g  A  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18   g  A  T  A  a 19 20 2 22 23 

TABLE 31 Bridge/Extender Oligonucleotides(SEQ ID NOs: 532-548, respectively in order of appearance)ON_Lam1aB7(rc)    .........................GTGCTGACTCAGCCACCCTC. 20 ON_Lam2aB7(rc)     ........................GCCCTGACTCAGCCTGCCTC. 20 ON_Lam31B7(rc)      .......................GAGCTGACTCAGG.ACCCTGC 20 ON_Lam3rB7(rc)     ........................GAGCTGACTCAGCCACCCTC. 70 ON_LamHf1cBrg(rc)  CCTCGACAGCGAAGTGCACAGAGCGTCTTGACTCAGCC....... 38ON_LamHf1cExt      CCTCGACAGCGAAGTGCACAGAGCGTCTTG............... 30 ON_LamHf2b2Brg(rc) CCTCGACAGCGAAGTGCACAGAGCGCTTTGACTCAGCC....... 30 ON_LamHf2b2Ext     CCTCGACAGCGAAGTGCACAGAGCGCTTTG............... 30 ON_LamHf2dBrg(rc)  CCTCGACAGCTAAGTGCACAGAGCGCTTTGACTCAGCC....... 38 ON_LamHf2dExt      CCTCGACAGCGAAGTGCACAGAGCGCTTTG............... 30 ON_LamHf31Brg(rc)  CCTCGACAGCGAAGTGCACAGAGCGAATTGACTCAGCC....... 30 ON_LamHf31Ext      CCTCGACAGCGAAGTGCACAGAGCGAATTG............... 30 ON_LamHf3rBrg(rc)  CCTCGACAGCGAAGTGCACAGTACGAATTGACTCAGCC....... 30 ON_LamHf3rExt      CCTCGACAGCGAAGTGCACAGTACGAATTG............... 30 ON_lamPlePCR       CCTCGACAGCGAAGTGCACAG........................ 21 ConSensus 

TABLE 32  Oligonucleotides used to make SSDNA locally double-stranded(SEQ ID NOs: 548-552, respectively in order of appearance) Adapters (8) H43HF3.1?02#1 5′-cc gtg tat tac tgt gcg aga g-3′ H43.77.97.1-03#2 5′-ct gtg tat tac tgt gcg aga g-3′H43.77.97.323#22 5′-cc gta tat tac tgt gcg aaa g-3′H43.77.97.230#23 5′-ct gtg tgt gcg aaa g-3′ H43.77.97.439#44 5′-ct tat tac tgt gcg aga c-3′H43.77.97.551#48 5′-cc atg tat tac tgt gcg aga c-3

TABLE 33  Bridge/extender pairs Bridges (2)  H43.XABr15′ggtgtagtgaTCTAGtgacaactctaagaatactctctacttgcagatgaacagCTTtAGggctgaggacaCTGCAGtctactattgtgcgaga-3′ (SEQ ID NO: 553)H43.XABr2  5′ggtgtagtgaTCTAGtgacaactctaagaatactctctacttgcagatgaacagCTTtAGagctgaggacaCTGCAGtctactattgtgcgaaa-3′  (SEQ ID NO: 554)Extender  H43.XAExt  5′ATAgTAgAcTqcAgTgTccTcAgcccTTAAgcTqTTcATcTgcAAgTAcTAcTAgTATTcTTAqAgTTgTcTcTAcTATcAcTAcAcc-3′   (SEQ ID NO: 555)

TABLE 34  PCR primers Primers H43.XAPCR2 gactgggTgTAgTgATcTAg (SEQ ID NO: 556) Hucmnest cttttctttgttgccgttagggtg (SEQ ID NO: 557) 

TABLE 35  PCR program for amplification of heavy chain CDR3 DNA95 degrees C.  5 minutes  95 degrees C. 20 seconds 60 degrees C. 30 seconds repeat 20x 72 degrees C.  1 minute 72 degrees C.  7 minutes   4 degrees C. hold Reagents (100 ul reaction):  Template            5 ul ligation mix 10x PCR buffer      1x  Taq                 5 U dNTPs             200 uM each  MyCl2               2 mM H43.XAPCR2-biotin 400 nM  Hucmnest          200 nM 

TABLE 36  Annotated sequence of CJR DY3F7(CJR-A05) 10251 bases ! ! Non-cutters  !  !BclI Tgatca    BsiWI Cgtacg   BssSI Cacgag !BstZ17I GTAtac BtrI CACgtg    EcoRV GATatc !FseI GGCCGGcc  HPaI GTTaac    MluI Acgcgt !PmeI GTTTaaac  PmlI CACgtg    PpuMI RGgwccv !RsrII CGgwccg  SapI GCTCTTC   SexAI Accwqgt !SgfI GCGATcgc  SgrAI CRccggyg SphI GOATGc  !StuI AGGcct    XmaI Cccggg !  ! cutters  ! ! Enzvmes that cut from 1 to 4 times and other features  ! !End at genes II and X               829!Start gene V                        843 !EsrGI Tgtaca                    1  1021 !BspMI Nnnnnnnnngcaggt           3  1104  5997  9183  (SEQ ID NO: 558) !-″- ACCTGCNNNNn                 1  2281  (SEQ ID NO: 559) !End of gene V                      1106 !Start gene VII                     1108 !BsaBI GATNNnnatc                2  1149  3967  (SEQ ID NO: 560) !Start gene IX                      1208 !End gene VII                       1211 !SnaBI TACgta                    2  1268  7133 !BspHI Tcatga                    3  1299  6085  7093 !Start gene VIII                    1301 !End gene IX                        1304 !End gene VIII                      1522 !Start gene III                     1578 !EagI Cggccg                     2  1530  8905 !XbaI Tctaga                     2  1643  8436 !KasI Ggcgcc                     4  1650  8724  9039  9120 !BsmI GAATGCN                    2  1769  9065 !BseRI GAGGAGNNNNNNNNNN          2  2031  8516  (SEQ ID NO: 561) !-″- NNnnnnnnnnctcctc            2  7603  8623  (SEQ ID NO: 562) !AlWNI CAGNNNctg                 3  2210  8072  8182 !BspDI ATcgat                    2  2520  9883 !NdeI CAtatg                     3  2716  3796  9847 !End gene III                       2846!Start gene VI                      2848 !AfeI AGCgct                     1  3032 !End gene VI                        3187 !Start gene I                       3189 !EarI CTCTTCNnnn                 2  1067  9271  (SEQ ID NO: 563) !-″- Nnnnnqaagag                 2  6126  8953  (SEQ ID NO: 564) !PacI TTAATtaa                   1  4125 !Start gene IV                      4213 !End gene I                         4235 !BsmFI Nnnnnnnnnnnnnnngtccc      2  5068  9515  (SEQ ID NO: 565) !MscI TGGcca                     3  5073  7597  9160 !PsiI TTAtaa                     2  5349  5837 !End gene IV                        5493 !Start ori                          5494 !NgoMIV Gccggc                   3  5606  8213  9315 !BanII GRGCYc                    4  5636  8080  8606  8889 !DraIII CACNNNgtg                1  5709 !DrdI GACNNNNnngtc               1  5752  (SEQ ID NO: 566) !AvaI Cycgrg                     2  5818  7240 !PvuII CAGctg                    1  5953 !BsmBI CGTCTCNnnnn               3  5964  8585  9271  (SEQ ID NO: 567) !End ori region                     5993 !BamHI Cgatcc                    1  5994 !HindIII Aagctt                  3  6000  7147  7384 !BciVI GTATCCNNNNNN              1  6077  (SEQ ID NO: 568) !Start bla                          6132 !Eco57I CTGAAG                   2  6238  7716 !SpeI Actagt                     1  6257 !BcgI gcannnnnntcg               1  6398  (SEQ ID NO: 569) !ScaI AGTact                     1  6442 !PvuI CGATcg                     1  6553 !FspI TGCgca                     1  6700 !BglI GCCNNNNnggc                3  6801  8208  8976  (SEQ ID NO: 570) !BsaT GGTCTCGgggg                1  6853  (SEQ ID NO: 571) !AhdI GACNNNnngtc                1  6920  (SEQ ID NO: 572) !Eam1105I GACNNNnngtc            1  6920  (SEQ ID NO: 573) !End bla                            6998 !AccI GTmkac                     2  7153  8048 !HincII GTYrac                   1  7153 !SalI Gtcqac                     1  7153 !XhoI Ctcgag                     1  7240 !Start PlacZ region                 7246 !End PlacZ region                   7381 !PflMI CCANNNNntgg               1  7382  (SEQ ID NO: 574) !RBS1                               7405 !Start M13-iii signal scq for LC    7418 !APaLI Gtgcac                    1  7470 !end M13-iii signal seq             7471 !Start light chain kappa L20:JK  1  7472 !Pf1FI GACNnngtc                 3  7489  8705  9099 !SbfI CCTGCAgg                   1  7542 !PstI CTGCAg                     1  7543 !KpnI GGTACc                     1  7581 !XcmI CCANNNNNnnnntgg            2  7585  9215  (SEQ ID NO: 575) !NsiI ATGCAt                     2  7626  9503 !BsgI ctgcac                     1  7809 !BbsI gtcttc                     2  7820  8616 !BlpI GCtnaac                    1  8017 !EspI GCtnagc                    1  8017 !EcoO109I RGgnccy                2  8073  8605 !Ecl136I GAGctc                  1  8080 !SacI GAGCTc                     1  8080 !End light chain                    8122 !AscI GGcgcgcc                   1  8126 !BssHII Gcgcgc                   1  8127 IRBS2                               8147 !SfiI GGCCNNNNnggcc              1  8207  (SEQ ID NO: 576) !NcoI Ccatgg                     1  8218 !Start 3-23, FR1                    8226 !MfeI Caattg                     1  8232 !BspEI Tccgga                    1  8298 !Start CDR1                         8316 !Statt FR2                          8331 !BstXI CCANNNNNntgg              2  8339  8812  (SEQ ID NO: 577) !EcoNI CCTNNnnnagg               2  8346  8675  (SEQ ID NO: 578) !Start FR3                          8373 !XbaI Tctac                      2  8436  1643 !AflII Cttaag                    1  8480!Start CDR3                         8520 !AatII GACGTc                    1  8556 !Start FR4                          8562 !PshAI GACNNnngtc                2  8573  9231  (SEQ ID NO: 579) !BstEII Ggtnacc                  1  8579 !Start CH1                          8595 !ApaI GGGCc                      1  8606!Bspl20I Gggccc                  1  8606 !PspOMI Gggccc                   1  8606 !AgeI Accggt                     1  8699 !Bsu361 CCtnagg                  2  8770  9509 !End of CH1                         8903!NOtI GCggccgc                   1  8904 !Start His6 tag                     8913  (SEQ ID NO: 12)!Start cMyc tag                     8931 !Amber codon                        8982 !NheI Gctagc                     1  8985 !Start M13 III Domain 3             8997 !NruI TCGcga                     1  9106 !BstBI TTcgaa                    1  9197 !EcoRI Gaattc                    1  9200 !XcmI CCANNNNNnnnntgg            1  9215  (SEQ ID NO: 580) !BstAPI GCANNNNntgc              1  9337  (SEQ ID NO: 581) !SacII CCGCgg                    1  9365 !End IIIstump anchor                9455 !AvrII Cctagg                    1  9462 !trp terminator                     9470 !SwaI ATTTaaat                   1  9784 !Start gene II                      9850 !BglII Agatct                    1  9936 !----------------------------------------------------------------------(SEQ ID NO: 582)      1 aat gct cct act att agt aga att gat gcc acc ttt tca gct cgc gcc !    gene ii continued     49 cca aat gaa aat ata gct aaa cag gtt att gac cat ttg cga act gta     97 tct cat ggt caa act aaa tct act cgt tcg cag act tgg gcc tcc act    145 gtt aTa tgg cat gaa act tcc aga cac cgt act tta gtt gca tat tta    193 aaa cat gtt gag cta cap caT Tat att cag caa tta agc tct aag cca    241 tcc gca aaa atg acc tct tat caa aag gag caa tta aag gta ctc tct    289 aat cct gac ctg ttg gag ttt gct tcc ggt ctg gtt cgc ttt gaa gct    337 cga att aaa acg cga tat ttg aag tct ttc ggg ctt cct ctt aat ctt    385 ttt gat gca atc cgc ttt gct tct gac tat aat agt cag ggt aaa gac    433 ctg att ttt gat tta tgg tca ttc tcg ttt tct aaa ctg ttt aaa gca    481 ttt gag ggg gat tca ATG cat att tat gac gat tcc gca gta ttg gac !                          Start gene x, ii continues    529 gct atc cag tct aaa cat ttt act att acc ccc tct ggc aaa act tct    577 ttt gca aaa gcc tct cgc tat ttt ggt ttt tat cgt cgt ctg gta aac    625 gag ggt tat gat agt gtt gct ctt act atg cct cgt aat tcc ttt tgg    673 cgt tat gta tct gca tta gtt gaa tgt ggt att cct aaa tct caa ctg    721 atg aat ctt tct acc tgt act aat gtt gtt ccg tta gtt cgt ttt att    769 aac gta gat ttt tct tcc caa cgt cct gac tgg tat aat gag cca gtt    817 ctt aaa atc gca TAA  !                      End X & II    832 ggtaattca ca  !  (SEQ ID NO: 626) !       M1              E5                 Q10                 T15    843 ATG att aaa gtt gaa att aaa cca tct caa gcc caa ttt act act cgt        Start gene V  !!      S17         S20                 P25                 E30    891 tct ggt gtt tct cgt ccg ggc cap cct tat tca ctg act gag cag ctt ! !              V35                 E40                 V45    939 tgt tac gtt gat ttg ggt aat gaa tat cog gtt ctt gtc aag att act ! !          D50                 A55                 L60    987 ctt gat gaa ggt cag cca gcc tat gcg cct ggt cTG TAC Acc gtt cat !                                                  BsrGI... !      L65                 V70                 S75                 R80   1035 ctg tcc tct ttc aaa gtt ggt cag ttc ggt tcc ctt atg att gac cgt ! !                      P85     K87 end of V   1083 ctg cgc ctc gtt ccg gct aag TAA C  !  1108 ATG gag cag gtc gcg gat ttc gat aca att tat cag gcg atg !      Start gene VII  !  1150 ata caa atc tcc gtt gta ctt tgt ttc gcg ctt ggt ata atc  !!                        VII and IX overlap.                          ..... S2  V3  L4  V5  (SEQ ID NO: 621)    S10   1192 gct ggg ggt caa agA TGA gt gtt tta gtg tat tot ttT gcc tct ttc gtt !                          End VII  !                        |start IX !      L13     W15                 G20                 T25             E29   1242 tta ggt tgg tgc ctt cgt apt ggc att acg tat ttt acc cgt tta atg gaa !   1293 act tcc tc !       .... stop of IX, IX and VIII overlap by four bases   1301 ATP aaa aag tct tta gtc ctc aaa gcc tct gta gcc gtt act acc ctc !      Start signal seauence of viii.  !   1349 gtt ccg atg ctg tct ttc gct gct gag ggt gac gat ccc gca aaa gcg !                                  mature VIII --->  1397 gcc ttt aac tcc ctg caa gcc tca gcg acc gaa tat atc ggt tat gcg   1445 tgg gcg atg gtt gtt gtc att   1466 gtc ggc gca act atc ggt atc aag ctg ttt aag  ! ! bases 1499-1539 are probable promoter for iii   1499 aaa ttc acc tcg aaa gca ! 1515  !       ...........  −35  .. !   1517 agc tga taaaccgat acaattaaag gctccttttg !                 ..... −10   ...  !  1552 gagccttttt ttt GGAGAt ttt ! S.D. uppercase, there may be 9 Ts  ! !         <------ III signal sequence ----------------------------->(SEQ ID NO: 583) !            M   K   K   L   L   F   A   I   P   L   V   V   P   F   1574 caac GTG aaa aaa tta tta ttc gca att cct tta gtt gtt cct ttc ! 1620 !  !       Y   S   G   A   A   E   S   H   L   D   G   A   1620 tat tct ggc gCG GCC Gas tca caT CTA GAc ggc gcc !                   EagI....         XbaI....  ! ! Domain 1 ------------------------------------------------------------            A   E   T   V   E   S   C   L   A   1656     gct gaa act gtt gaa agt tgt tta gca  ! !       K   S   H   T   E   I   S   F   T   N   V   W   K   D   D   K   T   1683 aaA Tcc cat aca gaa aat tca ttt aCT AAC GTC TGG AAA GAC GAC AAA ACt !!       L   D   R   Y   A   N   Y   E   G   S   L   W   N   A   T   G   V   1734 tta gat cgt tac gct sac tat gag ggC tgt ctg tgG AAT GCt aca ggc gtt !                                                    Bsmi.... !       V   V   C   T   G   D   E   T   Q   C   Y   G   T   W   V   P   I   1785 gta gtt tgt act ggt GAC GAA ACT CAG TGT TAC GGT ACA TGG GTT cct att !  !       G   L   A   I   P   E   N   1336 ggg ctt gct atc cct gaa aat  ! ! L1 linker ----------------------------------!       E   G   G   G   S   E   G   G   G   S   1857 gag ggt ggt ggc tct gag ggt ggc ggt tct  ! !       E   G   G   G   S   E   G   G   G   T  1887 gag ggt ggc ggt tct gag ggt ggc ggt act  ! !  Domain 2 -----------------------------------  1917 aaa cct cct gag tac ggt gat aca cct att ccg ggc tat act tat atc aac   1968 cct ctc gac ggc act tat ccg cct ggt act gag caa aac ccc gct aat cct   2019 aat cct tct ctt GAG GAG tct cag cct ctt aat act ttc atg ttt cag aat!                      BseRI..   2070 aat agg ttc cga aat agg cag ggg gca tta act gtt tat acg ggc act   2118 gtt act caa ggc act gac ccc gtt aaa act tat tac cag tac act cct   2166 gta tca tca aaa gcc atg tat gac gct tac tgg aac ggt aaa ttC AGA !                                                              AlwNI   2214 GAC TGc gct ttc cat tct ggc ttt aat gaG gat TTa ttT gtt tgt gas !       AlwNI   2262 tat caa ggc caa tcg tct gac ctg cct caa cct cct gtc sat gct   2307 ggc ggc ggc tct  !  start L2    2319 ggt ggt ggt tct   2331 ggt ggc ggc tct    2343 gag ggt ggt ggc tct gag gga ggc ggt tcc   2373 ggt ggt ggc tct ggt    ! end L2  !! Many published sequence of M13-derived phage have a longer linker ! than shown here by repeats of the EGGGS motif two more Limes. ! Domain 3  (SEQ ID NO: 584) ------------------------------------------------------------!       S   G   D   F   D   Y   E   K   M   A   N   A   N   K   G   A   2388 tcc ggt gat ttt gat tat gaa aag atg gca aac act aat aag ggg gct ! !       M   T   E   N   A   D   E   N   A   L   Q   S   D   A   K   G  2436 atg acc gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc  !!       K   L   D   S   V   A   T   N   Y   G   A   A   M   D   G   F   2484 aaa ctt gat tct gtc gct act gat tac ggt gct gct atc gat ggt ttc ! !       I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   D   2532 att ggt gac gtt tcc ggc ctt gct aat ggt aat ggt gct act ggt gat ! !       F   A   G   S   N   S   Q   M   A   Q   V   G   D   G   D   N   2580 ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt gat aat ! !       S   P   L   M   N   N   F   R   Q   Y   L   P   S   L   P   Q   2629 tca cct tta atg aat act ttc cgt cca tat tta cct tcc ctc cct caa ! !       S   V   E   C   R   P   F   V   F   N   A   G   K   P   Y   E   2676 tcg gtt gaa tat cgc cct ttt gtc ttt Ggc gct ggt aaa cca tat gaa ! !       F   S   I   D   C   D   K   I   N   L   F   R  2724 ttt tct att gat tgt gac aaa ata aac tta ttc cgt !                                                  End Domain 3  !!       G   V   F   A   F   L   L   Y   V   A   F   F   N   Y   V  F140   2760 ggt gtc ttt gct ttt ctt tta tat gtt gcc acc ttt atg tat gta ttt !      start transmembrane segment  ! !       S   T   F   A   N   I   L   2808 tct ccg ttt gct aac ata ctg  ! !       R   N   K   E   S    2629 cgt aat aag gag tct TAA ! stop of iii !     Intracellular anchor.  !     (SEQ ID NO: 585) !           M1 P2  V   L  L5   G   I   P   L  L10  L   R   F   L  G15   2847 tc ATG cca gtt ctt ttg ggt att ccg tta tta ttg cgt ttc ctc ggt !         Start VI  !  2894 ttc ctt ctg gta act ttg ttc ggc tat ctg ctt act ttt ctt aaa aag   2942 ggc ttc ggt act ata gct att gct att tca ttg ttt ctt gct ctt att   2990 att ggg ctt aac tca att ctt gtg ggt tat ctc tct gat att agc gct   3038 caa tta ccc tct gac ttt gtt cag ggt gtt cag tta att ctc ccg tct   3086 aat acg ctt ccc tgt ttt tat gtt att ctc tct gta aag act gct att   3134 ttc att ttt gac gtt aaa caa aaa atc gtt tct tat ttg gat tgg gat ! !                 M1  A2  V3      F5                 L10         G13   3182 aaa TAA t ATG gct gtt tat ttt gta act ggc aaa tta ggc tct gga !       end VI   Start gene 1  !  (SEQ ID NO: 586) !       K   T   L   V   S   V   G   K   I   Q   D   K   I   V   A   3228 aag acg ctc gtt agc gtt ggt aag att tag gat aaa att gta gct  ! !       G   C   K   I   A   T   N   L   D   L   R   L   Q   N   L   3273 ggg tgc aaa ata gca act aat ctt gat tta agg ctt caa aac ctc  ! !       P   Q   V   G   R   F   A   K   T   P   R   V   L   R   I   3318 ccg caa gtc ggg agg ttc gct aaa ccg cct cgc gtt ctt aga ata  !        P   D   K   P   S   I   S   D   L   L   A   I   G   R   G   3363 ccg aat aag cct tct ata tct gat ttg ctt gct att ggg cgc ggt  ! !       N   D   S   Y   D   E   N   K   N   G   L   L   V   L   D   3408 aat gat tcc tac gat gaa aat aaa aac ggc ttg ctt gtt ctc gat  !!       E   C   G   T   W   F   N   T   R   S   W   N   D   K   E   3453 gag tgc ggt act tgg ttt aat act cgt tct tgg aat gat aag gaa  ! !       R   Q   P   I   I   D   W   F   L   H   A   R   K   L   G   3498 aga tag ccg att att gat tgg ttt cta cat gct cgt aaa tta gga  ! !       W   D   I   I   F   L   V   Q   D   L   S   I   V   D   K   3543 tgg gat att att ttt ctt gtt tag gac tta tct att gtt gat aaa  ! !       Q   A   R   S   A   L   A   E   H   V   V   Y   C   R   R   3588 tag gcg cgt tct gca tta gct gaa cat gtt gtt tat tgt cgt cgt  !!       L   D   R   I   T   F   P   F   V   G   T   L   Y   S   L   3633 ctg gac aga att act tta cct ttt gtc ggt act tta tat tct ctt  ! !       I   T   G   S   K   M   P   L   P   K   L   H   V   G   V   3678 att act ggc tcg aaa atg cct ctg cct aaa tta cat gtt ggc gtt  !!       V   K   Y   G   D   S   Q   L   S   P   T   V   E   R   W   3723 gtt aaa tat ggc gat tct caa tta ago cct act gtt gag cgt tgg  ! !       L   Y   T   G   K   N   L   Y   N   A   Y   P   T   K   Q   3768 ctt tat act ggt aag aat ttg tat act gca tat gat act aaa cag  !!       A   F   S   S   N   Y   D   S   G   V   Y   S   Y   L   T   3813 gct ttt tct agt aat tat gat tcc ggt gtt tat tct tat tta ccg  ! !       P   Y   L   S   H   G   R   Y   F   K   D   L   N   L   G   3858 cct tat tta tca cac ggt cgg tat ttc aaa cca tta aat tta ggt  !!       Q   K   N   K   L   T   K   I   Y   L   K   K   F   S   R   3903 cag aag atg aaa tta act aaa ata tat ttg aaa aag ttt tct cgc  ! !       V   L   C   L   A   I   G   F   A   S   A   F   T   Y   S   3948 gtt ctt tgt ctt gcg att gga ttt gca tca gca ttt aca tat agt  ! !       Y   I   T   Q   P   K   P   E   V   K   K   V   V   S   Q   3993 tat ata acc caa cct aag ccg gag gtt aaa aag gta gtc tct tag  ! !       T   Y   D   F   D   K   F   T   I   D   S   S   Q   R   L   4082 acc tat gat ttt gat aaa ttc act att gac tct tct cag cgt ctt  ! !  4083 aat cta agc tat cgc tat gtt ttc aag gat tct aag gga aaa TTA!                                                              PacI  !!       I   N   S   D   D   L   Q   K   Q   G   Y   S   L   T   Y  4128 ATT AAt agc gac gat tta cag aag caa ggt tat tca ctc aca tat!     PacI !!      i I   D   L   C   T   V   S   I   K   K   G   N   S   N    E!     iv                                                      M1   K  4173  att gat tta tgt act gtt tcc att aaa aaa ggt aat tca aAT Gaa!                                                            Start IV    ! (SEQ ID NO: 527) !     i  I   V   K   C   N   .End of I !     iv  L3  L   N5  V   I7  N    F  V10    4218  att gtt aaa tgt aat TAA T TTT GTT !  IV continued.....  4243 ttc ttg atg ttt gtt tca tca tct tct ttt gct cag gta att gaa atg  4291 aat aat tcg cct ctg cgc gat ttt gta act tgg tat tca aag caa tca  4339 ggc gaa tcc gtt att gtt tct ccc gat gta aaa ggt act gtt act gta  4387 tat tca tct gac gtt aaa cct gaa aat cta cgc aat ttc ttt att tct  4435 gtt tta cgt gcA aat aat ttt gat atg gtA ggt tcT aAC cct tcc atT  4483 att cag aag tat aat cca aac aat cag gat tat att gat gaa ttg cca  4531 tca tct gat aat cag gaa tat gat gat aat tcc gct cct tct ggt ggt   4579 ttc ttt gtt ccg caa aat gat aat gtt act caa act ttt aaa att aat  4627 aac gtt cgg gca aag gat tta ata cga gtt gtc gaa ttg ttt gta aag  4675 tct aat act tct aaa tcc tca aat gta tta tct att gac ggc tct aat  4723 cta tta gtt gtt agt gcT cct aaa gat att tta gat aac ctt cct caa  4771 ttc ctt tcA act gtt gat ttg cca act gac cag ata ttg att gag ggt  4819 ttg ata ttt gag gtt cag caa ggt gat gct tta gat ttt tca ttt gct  4867 gct ggc tct cag cgt ggc act gtt gca ggc ggt gtt aat act gac cgc  4915 ctc acc tct gtt tta tct tct gct ggt ggt tcg ttc ggt att ttt aat  4963 ggc gat gtt tta ggg cta tca gtt cgc gca tta aag act aat agc cat  5011 tca aaa ata ttg tct gtg cca cgt att ctt acg ctt tca ggt cag aag  5059 ggt tct atc tct gtT GGC CAg aat gtc cct ttt att act ggt cgt gtg!                        MscI....  5107 act ggt gaa tct gcc aat gta aat aat cca ttt cag acg att gag cgt  5155 caa aat gta ggt att tcc atg agc gtt ttt cct gtt gca atg gct ggc  5203 ggt aat att gtt ctg gat att acc agc aag gcc gat agt ttg agt tct  5251 tct act cag gca agt gat gtt att act aat caa aga agt att gct aca  5299 acg gtt aat ttg cgt gat gga cag act ctt tta ctc ggt ggc ctc act  5347 gat tat aaa aac act tct caG gat tct ggc gta ccg ttc ctg tct aaa  5395 atc cct tta atc ggc ctc ctg ttt agc tcc cgc tct gat tcT aac gag  5443 gaa agc acg tta tac gtg ctc gtc aaa gca acc ata gta cgc gcc ctg  5491 TAG cggcgcatt  !      End IV  5503 aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc  5563 gcccgctcct ttcgctttct tcccttcctt tctcgccacg ttcGCCGGCt ttccccgtca!  5623 agctctaaat cgggggctcc ctttagggtt ccgatttagt gctttacggc acctcgaccc  5683 caaaaaactt gatttgggtg atggttCACG TAGTGggcca tcgccctgat agacggtttt!  5743 tcgccctttG ACGTTGGAGT Ccacgttctt taatagtgga ctcttgttcc aaactggaac!  5803 aacactcaac cctatctcgg gctattcttt tgatttataa gggattttgc cgatttcgga  5863 accaccatca aacaggattt tcgcctgctg gggcaaacca gcgtggaccg cttgctgcaa  5923 ctctctcagg gccaggcggt gaagggcaat CAGCTGttgc cCGTCTCact ggtgaaaaga!   5983 aaaaccaccc tGGATCC AAGCTT!                  BamHI  HindIII (1/2) !   Insert carrying bla gene   6006    gcaggtg gcacttttcg gggaaatgtg cgcggaaccc   6043 ctatttgttt atttttctaa atacattcaa atatGTATCC gctcatgaga caataaccct !                                           BciVI   6103 gataaatgct tcaataatat tgaaaaAGGA AGAgt !                                  RBS.?... !      Start bla gene   6138 ATG agt att caa cat ttc cgt gtc gcc ctt att ccc ttt ttt gcg gca ttt   6189 tgc ctt cct gtt ttt gct cac cca gaa acg ctg gtg aaa gta aaa gat gct   6240 gaa gat cag ttg ggC gcA CTA GTg ggt tac atc gaa ctg gat ctc aac agc !                            SpeI....!                       ApaLI & BssSI Removed   6291 ggt aag atc ctt gag agt ttt cgc ccc gaa gaa cgt ttt cca atg atg agc   6342 att ttt aaa gtt ctg cta tgt GGC GcG Gta tta tcc cgt att gac gcc ggg  6393 caa gaG CAA CTC GGT CGc cgC ATA cAC tat tct cag aat gac ttg gtt gAG !            BcgI............                                           ScaI  6444 TAC Tca cca gtc aca gaa aag cat ctt acg gat ggc atg aca gta aga gaa !      ScaI.   6495 tta tgc agt gct gcc ata acc atg agt gat aac act gcg gcc aac tta ctt   6546 ctg aca aCG ATC Gga gga cog aag gag cta acc gct ttt ttg cac aac atg !               Pvul....   6597 ggg gat cat gta act cgc ctt gat cgt tgg gaa ccg gag ctg aat gaa gcc   6648 ata cca aac gac gag cgt gac acc acg atg cct gta gca atg Gca aca acg   6699 tTG CCC Aaa cta tta act ggc gaa cta ctt act cta gct tcc cgg caa caa !       FspI....  !  6750 tta ata gac tgg atg gag gcg gat aaa gtt gca gga cca ctt ctg cac tcg   6801 GCC ctt ccG GCt ggc tgg ttt att gct gat aaa tct gga gcc ggt gag cgt !      BglI..........  6852 gGG TCT Cgc ggt atc att gca gca ctg ggg cca gat ggt aag ccc tcc cgt !       BsaI....   6903 atc gta gtt atc tac acG ACg ggg aGT Cag gca act atg gat gaa cga aat !                            AndI...........  6954 aga cag atc gct gag ata ggt gcc tca ctg att aag cat tgg TAA ctgt !                                                              stop   7003 caqaccaaqt ttactcatat atactttaaa ttqatttaaa acttcatttt taatttaaaa   7063 ggatctaggt gaagatcctt tttgataatc tcatgaccaa aatcccttaa cgtgagtttt   7123 cgttccactg tacgtaagac cccc   7147 AAGCTT   GTCGAC tgaa tggcgaatgg cgctttgcct !      HindIII SalI..  !      (2/2) HincII   7183 ggtttccggc accagaagog gtgccggaaa gctggctgga gtgcgatctt  !! Start of Fab-display cassette, the Fab DSR-A05, selected for ! binding to a protein antigen.  !    7233 CCTGAcG CTCGAG !      xBsu36I XhoI.. !  ! PlatZ promoter is in the following block  !   7246                         cgcaacgc aattaatgtg agttagctca   7274 ctcattaggc accccaggct ttacacttta tgcttccggc tcgtatqttg   7324 tgtggaattg tgagcggata acaatttcac acaggaaaca gctatgacca   7374 tgattacgCC AagcttTGGa gccttttttt tggagatttt caac !              PflMI....... !                 Hind3. (there are 3) ! Gene iii signal sequence: (Amino acid sequence is SEQ ID NO: 587) !        1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !       M   K   K   L   B   F   A   I   P   L   V   V   P   F   Y   7418 gtg aaa aaa tta tta ttc gca att cct tta gtt gtt cct ttc tat  !       16  17  18          Start light chain (L20:JK1) !       S   H   S   A   Q   D   I   Q   M   T   Q   S   P   A   7463 tct cac aGT GCA Caa gac atc cag atg acc cag tct cca gcc!              ApaLI... !              Sequence supplied bv extender !       T   L   S   L    7505 act ctg tct ttg  !!       S   P   G   E   R   A   T   L   S   C   R   A   S   Q   G   7517 tct cca ggg gaa aga gcc acc ctc tcc tgc agg gcc agt cag Ggt !!       V   S   S   Y   L   A   W   Y   Q   Q   K   P   G   Q   A  7562 gtt agc agc tac tta gcc tgg tac cag cag aaa cct ggc cag gct !!       P   R   L   L   I   Y   D   A   S   S   R   A   T   G   I  7607 ccc agg ctc ctc atc tat gAt gca tcc aAc agg gcc act ggc atc !!       P   A   R   F   S   G   S   G   P   G   T   D   F   T   L  7652 cca gCc agg ttc agt ggc agt ggg Cct ggg aca gac ttc act ctc !!       T   I   S   S   L   E   P   E   D   F   A   V   Y   Y   C  7697 acc atc agc agC ctA gag cct gaa gat ttt gca gtT tat tac tgt !!       Q   Q   R   S   W   H   P   W   T   F   G   Q   G   T   R  7742 cag cag CGt aAc tgg cat ccg tgg ACG TTC GGC CAA GGG ACC AAG !!       V   E   I   K   R   T   V   A   A   P   S   V   F   I   F  7787 gtg gaa atc aaa cga act gtg gCT GCA Cca tct gtc ttc atc ttc!                                   BsgI.... !!       P   P   S   D   E   Q   L   K   S   G   T   A   S   V   V  7832 ccg cca tct gat gag cag ttg aaa tct gga act gcc tct gtt gtg !!       C   L   L   N   N   F   Y   P   R   E   A   K   V   Q   W  7877 tgc ctg ctg aat aac ttc tat ccc aga gag gcc aaa gta cag ttg !!       K   V   D   N   A   L   Q   S   G   N   S   Q   E   S   V  7922 aag gtg gat aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc !!       T   E   R   D   S   K   D   S   T   Y   S   L   S   S   T  7967 aca gag cgg gac agc aag gac agc acc tac agc ctc agc agc acc !!       L   T   L   S   K   A   D   Y   E   K   H   K   V   Y   A  8012 ctg acG CTG AGC aaa gca gac tac gag aaa cac aaa gtc tac gcc!                EspI..... !!       C   E   V   T   H   Q   G   L   S   S   P   V   T   K   S  8057 tgc gaa gtc acc cat cag ggc ctG AGC TCg ccc gtc aca aag agc!                                    SacI.... !!       F   N   R   G   E   C   .   .  8102 ttc aac agg gga gag tgt taa taa !  8126     GGCGCG CCaattctat ttcaaGGAGA cagtcata!          AscI.....              RBS2.!        (Amino acid sequence is SEQ ID NO: 558)!       PelB signal sequence------(22 codons)----->!        1   2   3   4   5   6   7   8   9  10  11  12  13  14  15!       M   K   Y   L   L   P   T   A   A   A   G   L   L   L   L  8160 atg aaa tac cta ttg cct acg gca gcc gct gga ttg tta tta ctc !!      ...PelB signal------------> Start VH, FR1----------------->!       16  17  18  19  20  21  22  23  24  25  26  27  28  29  30!       A   A   Q   P   A   M   A   E   V   Q   L   L   E   S   G  8205 gcG GCC cag ccG GCC atg gcc gaa gtt CAA TTG tta gag tct ggt!        SfiI.............                 MfeI...!                       NcoI.... !!       31  32  33  34  35  36  37  38  39  40  41  42  43  44  45!       G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A  8250 ggc ggt ctt gtt cag cct ggt ggt tct tta cgt ctt tct tgc gct !!      ...FR1--------------------> CDR1--------------> FR2-------->!       46  47  48  49  50  51  52  53  54  55  56  57  58  59  60!       A   S   G   F   T   F   S   T   Y   E   M   R   W   V   R  8295 gct TCC GGA ttc act ttc tct act tac gag atg cgt tgg gtt cgC!          BspEI..                                               BstXI...! !       FR2--------------------------------------> CDR2 ---------->   !       61  62  63  64  65  66  67  68  69  70  71  72  73  74  75!       Q   A   P   G   K   G   L   E   W   V   S   Y   I   A   P  8340 CAa gct ccT GGt aaa ggt ttg gag tgg gtt tct tat atc gct cct!  BstXI............. !!       ...CDR2------------------------------------------> FR3---->!       76  77  78  79  80  81  82  83  84  85  86  87  88  89  90!       S   G   G   D   T   A   Y   A   D   S   V   K   G   R   F  8385 tct ggt ggc gat act gct tat gct gac tcc gtt aaa ggt cgc ttc !!       91  92  93  94  95  96  97  98  99 100 101 102 103 104 105!       T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M  8430 act atc TCT AGA gac aac tct aag aat act ctc tac ttg cag atg!              XbaI...!              Supplied by extender------------------------------- !!      -----------------------------------------FR3-------------->!      106 107 108 109 110 111 112 113 114 115 116 117 118 119 120!       N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   R  8475 aac agC TTA AGg gct gag gac act gca gtc tac tat tgt gcg agg!            AflII...!      from extender---------------------------------> !!      CDR3--------------------------------------------------> FR4-->!      121 122 123 124 125 126 127 128 129 130 131 132 133 134 135!       R   L   D   G   Y   I   S   Y   Y   Y   G   M   D   V   W  8520 agg ctc gat ggc tat att tcc tac tac tac ggt atg GAC GTC tgg ! !!      136 137 138 139 140 141 142 143 144 145!       G   Q   G   T   T   V   T   V   S   S    8565 ggc caa ggg acc acG GTC ACC gtc tca agc!                        BstEII... ! !      CH1 of IgG1---------->!       A   S   T   K   G   P   S   V   F   P   L   A   P   S   S   8595 gcc tcc acc aag ggc cca tcg gtc ttc ccc ctg gca ccc tcc tcc !!       K   S   T   S   G   G   T   A   A   L   G   C   L   V   K  8640 aag agc acc tct ggg ggc aca gcg gcc ctg ggc tgc ctg gtc aag !!       D   Y   F   P   E   P   V   T   V   S   W   N   S   G   A  8685 gac tac ttc ccc gaa ccg gtg acg gtg tcg tgg aac tca ggc gcc  !!       L   T   S   G   V   H   T   F   P   A   V   L   Q   S   S  8730 ctg acc agc ggc gtc cac acc ttc ccg gct gtc cta cag tCC TCA!                                                           Bsu36I.... !!       G   L   Y   S   L   S   S   V   V   T   V   P   S   S   S  8775 GGa ctc tac tcc ctc agc agc gta gtg acc gtg ccc tcc agc agc!  Bsu36I.... !!       L   G   T   Q   T   Y   I   C   N   V   N   H   K   P   S  8820 ttg ggc acc cag acc tac atc tgc aac gtg aat cac aag ccc agc !!       N   T   K   V   D   K   K   V   E   P   K   S   C   A   A  8865 aac acc aag gtg gac aag aaa gtt gag ccc aaa tct tgt GCG GCC!                                                          NotI...... !!       A   H   H   H   H   H   H   G   A   A   E   Q   K   L   I  8910 GCa cat cat cat cac cat cac ggg gcc gca gaa caa aaa ctc atc!  ..NotI.... H6 tag................. Myc-Tag........................ !!       S   E   E   D   L   N   G   A   A   q   A   S   S   A  8955 tca gaa gag gat ctg aat ggg gcc gca tag GCT AGC tct gct!      Myc-Tag....................         ... NheI...!                                         Amber ! ! III′stump !! Domain 3 of III -------------------------------------------------------!       S   G   D   F   D   Y   E   K   M   A   N   A   N   K   G   A  8997 agt ggc gac ttc gac tac gag aaa atg gct aat gcc aac aaa GGC GCC!      tcc   t   t   t   t   t   a   g       a   c   t   t   g   g   t !W.T.!                                                              KasI...(2/4)! !       M   T   E   N   A   D   E   N   A   L   Q   S   D   A   K   G  9045 atG ACT GAG AAC GCT GAC GAG aat gct ttg caa agc gat gcc aag ggt!            c   a   t   c   t   a   c   g c a   g tct   c   t   a   c !W.T.! !       K   L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F  9093 aag tta gac agc gTC GCG Acc gac tat GGC GCC gcc ATC GAc ggc ttt!        a c t   t tct       t   t   t   c   t   t   t       t   t   c !W.T.!                       NruI....           KasI...(3/4) !!       I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   D  9141 atc ggc gat gtc agt ggt tTG GCC Aac ggc aac gga gcc acc gga gac!        t   t   c   t tcc   c c t   t   t   t   t   t   t   t   t   t !W.T.!                               MscI...(3/3) !!       F   A   G   S   N   S   Q   M   A   Q   V   G   D   G   D   N  9189 ttc GCA GGT tcG AAT TCt cag atg gcC CAG GTT GGA GAT GGg gac aac!        t   t   c   t       c   a       t   a   c   t   c   t   t   t !W.T.!          BspMI.. (2/2)                 XcmI................!                    EcoRI... !!       S   P   L   M   N   N   F   R   Q   Y   L   P   S   L   P   Q  9237 agt ccg ctt atg aac aac ttt aga cag tac ctt ccg tct ctt ccg cag!      tca   t t a       t   t   c c t   a   t t a   t   c   c   t   a !W.T.! !       S   V   E   C   R   P   F   V   F   S   A   G   K   P   Y   E  9285 agt gtc gag tgc cgt cca ttc gtt ttc tct gcc ggc aag cct tac gag!      tcg   t   a   t   c   t   t   c   t agc   t   t   a   a   t   a !W.T.! !   9333 ttc aGC Atc gac TGC gat aag atc aat ctt ttC CGC!        t tct   t   t   t   c   a   a   c t a   c   t !W.T.!           BstAPI........                       SacII...!                                                  End Domain 3 ! !  9369 GGc gtt ttc gct ttc ttg cta tac gtc gct act ttc atg tac gtt ttc!        t   c   t   g   t c t t a   t   t   c   c   t       t   a   t !W.T.!      start transmembrane segment !!       S   T   F   A   N   I   L     R   N   K   E   S  9417 aGC ACT TTC GCC AAT ATT TTA   Cgc aac aaa gaa agc!      tct   g   t   t   c   a c g     t   t   g   g tct !W.T.!                                    Intracellular anchor. !!               .   .   9453         tag tga tct CCT AGG!                          AvrII.. !  9468 aag ccc gcc taa tga gcg ggc ttt ttt ttt ct  ggt!        | Trp terminator                     |           !! End Feb cassette  !  9503   ATGCAT CCTGAGG ccgat actgtcgtcg tcccctcaaa ctggcaaatg !        NsiI.. Bsu36I.(3/3)   9551 cacggttacg atgcgcccat ctacaccaac gtgacctatc ccattacggt caatccaccg   9611 tttgttccca cggagaatcc gacgggttgt tactcgctca catttaatgt tgatgaaagc   9671 tggctacagg aaggccagac gcgaattatt tttgatggcg ttcctattgg ttaaaaaatg   9731 agctgattta acaaaaattt aaTgcgaatt ttaacaaaat attaacgttt acaATTTAAA !                                                                SwaI...   9791 Tatttgctta tacaatcttc ctatttttgg ggcttttctg attatcaacc GGGGTAcat   9850 ATG att gac atg cta gtt tta cga tta cog ttc atc gat tc t ctt gtt tgc !      Start gene II   9901 tcc aga ctc tca ggc aat gac ctg ata gcc ttt gtA GAT CTc tca aaa ata !                                                    BglII...   9952 gct acc ctc tcc ggc atT aat tta tca act aga acg gtt gaa tat cat att  10003 gat ggt gat ttg act gtc tcc ggc ctt tct cac cct ttt gaa tct tta cct  10054 aca cat tac tca ggc att gca ttt aaa ata tat gag ggt tct aaa aat ttt  10105 tat cct tgc att gaa ata aag gct tct ccc gca aaa gta tta cag ggt cat  10156 aat gtt ttt ggt aca acc gat tta gct tta tgc tct gag gct tta ttg ctt  10207 aat ttt gct aat tct tta cct tgc ctg tat gat tta ttg aat gtt ! ! gene II continues  !  !----------------------

TABLE 37 ! DNA seq of w.t. M3 gene iii  ! (Nucleotide sequence is SEQ ID NO: 590; Amino acid sequene is SEQ ID NO: 591) !        1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !       fm   K   K   L   L   F   A   I   P   L   V   V   P   F   Y   1579  gtg aaa aaa tta tta ttc gca att cct tta gtt gtt cot ttc tat !       Signal sequence............................................!       16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !       S   E   S   A   K   T   V   E   S   C   L   A   K   P   H   1624 tct cac tcc gct gaa act gtt gaa agt tgt tta gca aaa ccc cat ! Signal sequence> Domain 1---------------------------------------  !!       31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !       T   E   N   S   F   T   N   V   W   K   D   D   K   T   L   1669 aca gaa act tca ttt act aac gtc tgg aaa gac gac aaa act tta !      Domain 1---------------------------------------------------!       46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !       D   R   V   A   N   Y   E   G   C   L   W   N   A   T   G   1714 gat cgt tac gct aac tat gag ggt tgt ctg tgG AAT GCt aca ggc !                                                BsmI.... !      Domain 1---------------------------------------------------!       61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !       V   V   V   C   T   G   D   E   T   Q   C   Y   G   T   W   1759 gtt ata gtt tgt act ggt gac gas act cag tgt tac ggt aca tgg !      Domain 1  !!       76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !       V   P   I   G   L   A   I   P   E   N   E   G   G   G   S   1804 gtt cct att ggg ctt gct atc cct gaa aat gag ggt ggt ggc tct !      Domain 1------------------------------> Linker 1-----------  !!       91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !       E   G   G   G   S   E   G   G   G   S   E   G   G   G   T   1849 gag ggt ggc ggt tot gag ggt ggc ggt tct gag ggt ggc ggt act !      Linker 1--------------------------------------------------> !!      106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !       K   P   P   E   Y   G   D   T   P   I   P   G   Y   T   Y   1894 aaa cct cct gag tac ggt gat aca cot att ccg ggc tat act tat !      Domain 2---------------------------------------------------!      121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !       I   N   P   L   D   G   T   Y   P   P   G   T   E   Q   N   1939 atc aac cct ctc gac ggc act taT CCG CCt ggt act gag caa aac !      Domain 2---------------------------------------------------!      136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !       P   A   N   P   N   P   S   L   E   E   S   Q   P   L   N   1984 ccc gct act cct act cct tct ctt GAG GAG tct cag cct ctt act !                                      BseRI..  !      Domain 2 !      151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !       T   F   M   F   Q   N   N   R   F   R   N   R   Q   C   A   2029 act ttc atg ttt cag act act agg tcc oga aat agg cag ggg gca !      Domain 2--------------------------------------------------- !!      166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !       L   T   V   Y   T   G   T   V   T   Q   G   T   D   P   V   2074 tta act gtt tat acg ggc act gtt act caa ggc act gac ccc gtt !      Domain 2--------------------------------------------------- !!      181 132 183 184 185 186 137 188 189 190 191 192 193 194 195 !       K   T   Y   Y   Q   Y   T   P   V   S   S   K   A   M   Y   2119 aaa act tat tac cag tac act cot gta tca toa aaa gcc atg tat !    Domain 2----------------------------------------------------- !!      196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !       D   A   Y   W   N   G   K   E   R   D   C   A   F   H   S   2164 gac gct tac tgg aac ggt aaa ttC AGa gaC TGc gct ttc cat tct !                                    AlwNI.......!      Domain 2--------------------------------------------------- ! !      211 212 213 214 215 216 217 214 219 220 221 222 223 224 225 !       G   E   N   E   D   P   F   V   C   E   Y   Q   G   Q   S   2209 ggc ttt aat gaG GAT CCa ttc gtt tgt gaa tat caa ggc caa tcg !                    BamHI... !      Domain 2--------------------------------------------------- !!      226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !       S   D   L   P   Q   P   P   V   N   A   G   G   G   S   G   2254 tct gac ctg cct caa cct cct gtc aat gct ggc ggc ggc tct ggt !      Domain 2------------------------------> Linker 2-----------  !!      241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 !       G   G   S   G   G   G   S   E   G   G   G   S   E   G   G   2299 ggt ggt tot ggt ggc ggc tot gag ggt ggt ggc tct gag ggt ggc        Linker 2--------------------------------------------------- ! !      256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 !       G   S   E   G   G   G   S   E   G   G   G   S   G   G   G   2344 ggt tct gag ggt ggc ggc tct gag gga ggc ggt tcc ggt ggt ggc !      Linker 2--------------------------------------------------- ! !      271 272 273 274 275 276 277 273 279 280 231 282 283 284 285 !       S   G   S   G   D   F   D   Y   E   K   M   A   N   A   N   2389 tct ggt tcc ggt gat ttt gat tat gaa aag atg gca aac gct aat !Linker 2>     Domain 3-------------------------------------------  !       286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 !       K   G   A   M   T   E   N   A   D   E   N   A   L   Q   S   2434 aag ggg got atg acc gaa aat gcc gat gaa aac gog cta cag tCt !      Domain 3--------------------------------------------------- ! !      301 302 303 304 305 306 307 308 309 310 311 312 313 314 315!       D   A   K   G   K   L   D   S   V   A   T   D   Y   G   A  2479 gac gct aaa ggc aaa ctt gat tct gtc gct act gat tac ggt gct !      Domain 3--------------------------------------------------- ! !      316 317 319 319 320 321 322 323 324 325 326 327 328 329 330 !       A   I   D   G   F   I   G   D   V   S   G   L   A   N   G   2524 gct atc gat ggt ttc att ggt gac gtt tcc ggc ctt gct aat ggt !      Domain 3--------------------------------------------------- ! !      331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 !       N   C   A   T   G   D   F   A   C   S   N   S   Q   M   A   2569 aat ggt gct act ggt gat ttt got ggc tct aat tcc caa atg gct !      Domain 3---------------------------------------------------!      346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 !       Q   V   G   D   G   D   N   S   P   L   M   N   N   E   R   2614 caa gtc ggt gac ggt gat aat tca cct tta atg aat aat ttc cgt !      Domain 3--------------------------------------------------- !!      361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 !       Q   Y   L   P   S   L   P   Q   S   V   E   C   R   P   F   2659 caa tat tta cct tcc ctc cct caa tcg gtt gaa tgt cgc cct ttt !      Domain 3---------------------------------------------------  ! !      376 377 378 379 330 381 382 383 384 385 386 387 338 389 390 !       V   E   S   A   G   K   P   Y   E   F   S   I   D   C   D   2704 gtc ttt agc gct ggt aaa cca tat gaa ttt tct att gat tat gac !      Domain 3---------------------------------------------------!      391 392 393 394 395 396 391 398 399 400 401 482 493 494 405 !       K   I   N   L   F   R   G   V   F   A   F   L   L   Y   V   2749 aaa ata aac tta ttc cgt ggt gtc ttt gcg ttt ctt tta tat gtt !      Domain 3--------------> Transmembrane segment  !!      406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 !       A   T   E   M   Y   V   E   S   T   F   A   N   I   L   R   2794 gcc acc ttt ata tat gta ttt tct acg ttt gct aac ata ctg cgt !      Transmembrane segment---------------------------------> ICA-- !      421 422 423 424 425  !       N   K   E   S   .   2339 aat aag gag tct taa ! 2853 !      ICA----------->            ICA = intracellular anchor !------------------ End of Table -----------------------------------------

TABLE 36  Whole mature III anchor M13-IIIderived anchor with recoded DNA !  !         1   2   3 !         A   A   A (SEQ ID NO: 594)      1   GCG gcc gca (SEQ ID NO: 593)  !        NotI......  !!         4   5   6   7   8   9  10  11  12  13  14  15  16  17 !         H   H   H   H   H   H   G   A   A   E   Q   K   L   I     10   cat cat cat cac cat cac ggg gcc gca gaa caa aaa ctc atc  ! !        18  19  20  21  22  23  24  25  26  27  28  29 !         S   E   E   D   L   N   G   A   A   .   A   S     52   tca gaa gag gat ctg act ggg gcc gca Tag GCT AGC !                                                NheI...  ! !        30  31  32  33  34  35  36  37  38  39 !         D   I   N   D   D   R   M   A   S   T     88   GAT ATC aac gat gat cgt atg gct tct act ! (ON_C37bot) [RC] 5′-c aac gat gat cgt atg gcG CAt Gct gcc gag aca g-3′!        EcoRV..              (SEQ ID NO: 592) !        Enterokinase cleavage site. !  Start mature III (recoded) Domain 1 ---->!              40  41  42  43  !               A   E   T   V    118        |gcC|gaG|acA|gtC|  !                t   a   t   t ! W.T. !        44  45  46  47  48  49  50  51  52  53  54  55  56  57  53 !         E   S   C   L   A   K   P   H   T   E   N   S   F   I   N    130  |gaa|TCC|tgC|CTG|GCC|AaG|ccT|caC|acT|gaG|aat|AGT|ttC|aCA|Aat| !            agt   t t a   a   a   c   t   a   a     tce   t   t   c ! W.T. !                     MscI....  !!        59  60  61  62  63  64  65  66  67  68  69  70  71  72  73 !         V   W   K   D   D   K   I   L   D   R   Y   A   N   Y   E    175  |gtg|TGG|aaG|gaT|gaT|aaG|acC|CtT|gAT|CGA|TaT|gcC|aaT|taC|gaA| !          c       a   c   c   a   t t a       t   c   t   c   t   g ! W.T. !                                         BspDI... !        74  75  76  77  78  79  80  81  82  83  84  85  86  87  88 !         G   C   L   W   N   A   T   G   V   V   V   C   T   G   D    220  |ggC|tqC|TtA|tgg|aat|gcC|ACC|GGC|GtC|gtT|gtC|TGC|ACG|ggC|gaT|           t   t c g           t   a       t   a   t   t   t   t   c ! W.T. !                              SgrAT......         BsgI....  !!        89  90  91  92  93  94  95  96  97  98  99  100 101 102 103 !         E   T   Q   C   Y   G   T   W   V   P   I   G   L   A   I    265  |gaG|acA|caA|tgC|taT|ggC|ACG|TGg|atG|ccG|atA|gGC|TTA|GCC|atA| !          a   t   a   t   c   t   a       t   t   t   g c t   t   c ! W.T. !                              PmlI....               BlpT..... !!     Domain 1-----> Linker 1---------------->!        104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 !         P   E   N   E   G   G   G   S   E   G   G   G   S   E   G    310  |ccG|gaG|aaC|gaA|ggC|ggT|ggT|AGC|gaA|ggC|ggT|ggC|AGC|gaA|ggC| !          t   a   t   g   t   t   c tct   g   t   c   t tct   g   t ! W.T. !  !        Linker 1----------------------> Domain 2--------------->!        119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 !         G   G   S   E   G   G   G   T   H   P   P   E   Y   G   D    355  |ggT|GGA|TCC|gaA|ggA|ggT|ggA|acC|aaG|ccG|ccG|gaA|taT|ggC|gaC| !          c   t   t   g   t   c   t   t   a   t   t   g   c   t   t ! W.T. !            BamHI..(2/2)  !         134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 !         T   P   I   P   G   Y   T   Y   I   N   P   L   D   G   T    400  |acT|ccG|aCA|CCT|GGT|CaC|acC|CaC|aCT|aaT|ccG|TCA|gaT|ggA|acC|!          a   t   t   g   a   t   t   t   c   c   t c c   c   c   t ! W.T. !                  SexAI....  !!        149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 !         Y   P   P   G   T   E   Q   N   P   A   N   P   N   P   S    445  |taC|ccT|ccG|ggC|acC|gaA|caG|aaT|ccT|gcC|aaC|ccG|aaC|ccA|AGC|!          T   G   t   t   t   g   a   c   c   t   t   t   t   t tct ! W.T. !                                                              Hindiii... ! !       164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 !        L   E   E   S   Q   P   L   N   T   F   M   F   Q   N   N    490 |TTA|gaA|gaA|AGC|caA|ccG|TtA|aaC|acC|ttT|atg|ttC|caA|aaC|aaC|!       c t   G   G tct   g   t c t   t   t   c       t   g   t   t ! W.T. ! HindIII.  !!       179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 !        R   F   R   N   R   Q   G   A   L   T   V   Y   T   G   T    535 |CgT|ttT|AgG|aaC|CgT|caA|gGT|GCT|CtT|acC|gTG|TAC|AcT|ggA|acC| !       a g   c c a   t a g   g   g   a t a   t   t   t   g   c   t ! W.T. !                                HgiAI...        BsrGI...         194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 !        V   T   Q   G   T   D   P   V   K   T   F   Y   Q   Y   T    580 |gtC|acC|caG|GGT|ACC|gaT|ccT|gtC|aaG|acC|taC|taT|caA|taT|acC|!         t   t   a   c   t   c   c   t   a   t   t   c   g   c   t ! W.T. !                   KpnI...  !!       209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 !        P   V   S   S   K   A   N   Y   D   A   Y   W   N   G   K    625 |ccG|gtC|TCG|AGt|aaG|gcT|atg|taC|gaT|gcC|taT|tgg|aaT|ggC|aaG|!         t   a   a tca   a   c       t   c   t   c       c   t   a ! W.T. !         BaaI....  !             XhoI.... !!       224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 !        F   R   D   C   A   F   H   S   G   F   N   E   D   P   F    670 |ttT|CgT|gaT|tgT|gcC|ttT|caC|AGC|ggT|ttC|aaC|gaa|gac|CCt|ttT|!         C A a   C   c   t   c   t tct   c   t   t   G   T   a   c ! W.T. ! !       239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 !        V   C   E   Y   Q   G   Q   3   S   D   L   P   Q   P   P    715 |gtC|tgC|gaG|taC|caG|ggT|caG|AGT|AGC|gaT|TtA|ccG|caG|ccA|CCG|!         t   t   a   t   a   c   a tcg tct   c c g   t   a   t   t ! W.T. ! DrdI.....                                                   AgeI..... ! !  Domain 2-------->  Linker 2--------------------->!       254 255 256 257 258 259 260 251 262 263 264 255 266 267 268 !        V   N   A   C   C   C   S   C   C   C   S   C   C   C   S    760 |GTT|AAC|gcG|ggT|ggT|ggT|AGC|ggC|ggA|ggC|AGC|ggC|ggT|ggT|AGC| !         c   t   t   c   c   c tct   t   t   t tct   t   c   c tct ! W.T. ! ApeI.....  !        HpaI...  !        HincII.  ! !       Linker 2----------------------------------------------> Domain 3-->!       269 270 271 272 273 274 275 276 277 278 279 200 281 282 283 !        E   G   G   G   S   E   G   G   G   S   G   G   G   S   G    805 |gaA|ggC|ggA|ggT|AGC|gaA|ggA|ggT|ggC|AGC|ggA|ggC|ggT|AGC|ggC| !         g   t   t   c tct   g   t   c   t tct   g   t   c tct   t  ! W.T. ! !       ------------Domain 3------------------->!       284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 !        S   G   D   F   D   Y   E   K   M   A   N   A   N   K   G    850 |AGT|ggC|gac|ttc|gac|tac|gag|aaa|atg|gct|aat|gcc|aac|aaa|GGC| !       tcc   t   t   t   t   t   a   g       a   c   t   t   g   g ! W.T. !                                                               KasI.... !  !       299 300 301 302 302 304 305 306 307 308 309 310 311 312 313 !        A   M   T   E   N   A   D   E   N   A   L   Q   S   D   A    895 |GCC|atg|act|gag|aac|gct|gac|gaG|AAT|GCA|ctg|caa|agt|gat|gCC| !         t       c   a   t   c   t   a   c   g   a   g tct   c   t ! W.T. !  KasI....                           BsmI....                   StyI... ! !       314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 !        K   G   K   L   D   S   V   A   T   D   Y   G   A   A   I    940 |AAG|GGt|aag|tta|gac|agc|gTC|GCc|Aca|gac|tat|ggT|GCt|gcc|atc| !         a   c   a c t   t tct       t   t   t   c           t     ! W.T. !  StyI......           PflFT...... !!       329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 !        D   G   F   I   G   D   V   S   G   L   A   N   G   N   G    985 |gac|ggc|ttt|atc|ggc|gat|gtc|aat|ggt|ctg|act|aac|ggc|aac|gga| !         t   t   c   t   t   c   t tcc   c c t       t   t   t   t ! W.T. ! !       344 345 346 347 348 349 350 351 352 353 !        A   T   G   D   F   A   G   S   N   S   1030 |gcc|acc|gga|gac|ttc|GCA|GGT|tcG|AAT|TCt| !         t   t   t   t   t   t   c   t       c ! W.T. !                                 BstBI... !                                     EcoRI... !                           BspMI..  ! !       354 355 356 357 358 359 360 361 362 363 !        Q   M   A   Q   V   G   D   G   D   N   1060  cag atg gcC CAG GTT GGA GAT GGa gac aac !         a       t   a   c   t   c   t   t   t ! W.T. !                 XcmI................  ! !       364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379!        S   P   L   M   N   N   F   R   Q   Y   L   P   S   L   P   Q   1090  agt ccg ctt atg aac aac ttt aga tag tac ctt ccg tct ctt ccg cag !       tca   t t a       t   t   c c t   a   t t a   t   c   c   t   a ! W.T. ! !       380 381 392 333 384 385 386 397 328 389 390 391 392 393 394 395 !        S   V   E   C   R   P   F   V   F   S   A   G   K   P   Y   E   1138  agt gtc gag tgc cgt cca ttc gtt ttc tct gcc ggc aag cct tac gaa !       tcg   t   a   t   c   t   t   c   t agc   t   t   a   a   t   a ! W.T. !  !       Domain 3-------------------------------------->!       396 397 398 399 400 401 402 403 404 405 406 407 !        F   S   I   D   C   D   K   I   N   L   F   R   1186  ttc aGC Atc gac TGC gat aag atc aat ctt ttC CGC !        t tct   t   t   t   c   a   a   c t a       t !           BRtAPI........                       SacII...  !!       transmembrane segment-------------> !       408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 !        G   V   F   A   F   L   L   Y   V   A   T   F   M   F   V   F   1222  GGc gtt ttc gct ttc ttg cta tac gtc gct act ttc atg tac gtt ttc !         t   c   t   g   t c t t a   t   t   c   c   t       t   a   t ! W.T. ! !       424 425 426 427 428 429 430   431 432 433 434 435 !        S   T   F   A   N   I   L     R   N   K   E   S   1270  aGC ACT TTC GCC AAT ATT TTA   Cgc aac aaa gaa agc !       tct   g   t   t   c   a c g     t   t   g   g tct ! W.T. !                                     Intracellular anchor. !                .   .   1306          tag tga tct CCT AGG!                          AvrII..  !  1321  aag ccc gcc taa tga gcg ggc ttt ttt ttt ct ggt !         | Trp terminator                     |  ! End Fab cassette !------------------------------End of Table ------------------------

TABLE 39  ONs to make deletions in III ! ONs for use with NheI !                                                                          N(SEQ ID NO: 595) (ON_G29bot)                         5′-c aTT gAT ATc gct Agc cTA Tgc-3′  !22 ! this is the reverse complement of 5′-aca tag gct agc gat atc aac g-3′ !                                              NheI... scab.........(ON_G104top) 5′-g|ata|ggc|tta|gcT|aGC|ccg|gag|aac|gaa|gg-3′             ! 30(SEQ ID NO: 596) !            Scab.............NheI... 104 105 106 107 108 (ON_G236top) 5′-c|ttt|cac|agc|ggt|ttc|GCT|AGC|gac|cct|ttt|gtc|tgc-3′    ! 37(SEQ ID NO: 597) !                                     NheI... 236 237 238 239 240 (ON_G236tCS) 5′-c|ttt|cac|agc|agt|ttc|GCT|AGC|gac|cct|ttt|gtc|Agc- !                                     NheI... 236 237 238 239 240                 gag|tac|cag|ggt|c-3′ (SEQ ID NO: 598)  ! 50 ! ONs for use with Sph1 G CAT Gc (ON_X37bot)       5′-gAc TgT cTc ggc Agc ATg cgc cAT Acg ATc ATc gTT g-3′! 37 (SEQ ID NO: 599) !                       N   D   D   R   M   A   H   A  (SEQ ID NO: 601) !(ON_X37bot)=[RC] 5′-c aac gat gat cgt atg gcG CAt Gct gcc gag aca gtc-3′                              (SEQ ID NO: 600) !                                          SphI....Scab.............(ON_X104top) 5′-g|gtG ccg|ata|ggc|ttG|CAT|GCa|ccg|gag|aac|gaa|gg-3′ ! 36 (SEQ ID NO: 617) !                Scab...............SphI....   104 105 106 107 108(ON_X-236top) 5′-c|ttt|cac|agc|ggt|ttG|CaT|gCa|gac|cct|ttt|gtc|tgc-3′ ! 37 (SEQ ID NO: 602) !                               SphI.... 236 237 238 239 240 (ON_X236tCS) 5′-c|ttt|cac|agc|ggt|ttG|CaT|aCa|gac|cct|ttt|atc|Agc- !                                     NheI... 236 237 238 239 240                 gag|tac|cag|ggt|c-3′ (SEQ ID NO: 603)  ! 50 

TABLE 40 Phage titers and enrichments of a selections with aDY3F31-based human Fab library Input Output Output/input (total cfu)(total cfu) ratio R1-ox 4.5 × 10¹² 3.4 × 10⁵ 7.5 × 10⁻⁸ selected onphOx-BSA R2-Strep 9.2 × 10¹² 3 × 10⁸ 3.3 × 10⁻⁵ selected on Strep-beads

TABLE 41 Frequency of ELISA positives in DY3F31-based Fab librariesAnti- 9E10/ Anti- M13 RAM- CK/CL HRP HRP Gar-HRP R2-ox (with IPTGinduction) 18/44 10/44 10/44 R2-ox (without IPTG) 13/44 ND ND R3-strep(with IPTG) 39/44 38/44 36/44 R3-strep (without IPTG) 33/44 ND ND

1.-116. (canceled)
 117. A method for preparing single-stranded nucleicacids, the method comprising the steps of: (i) contacting asingle-stranded nucleic acid sequence that has been cleaved with arestriction endonuclease with a partially double-strandedoligonucleotide, the single-stranded region of the oligonucleotide beingfunctionally complementary to the nucleic acids in the region thatremains after cleavage, the double-stranded region of theoligonucleotide including any sequences necessary to return thesequences that remain after cleavage into proper and original readingframe for expression and containing a restriction endonucleaserecognition site 5′ of those sequences; and (ii) cleaving the partiallydouble-stranded oligonucleotide sequence solely at the restrictionendonuclease recognition site contained within the double-strandedregion of the partially double-stranded oligonucleotide, the contactingand the cleaving steps being performed at a temperature sufficient tomaintain the nucleic acid in substantially single-stranded form, theoligonucleotide being functionally complementary to the nucleic acidover a large enough region to allow the two strands to associate suchthat cleavage may occur at the chosen temperature and at the desiredlocation, and the cleavage being carried out using a restrictionendonuclease that is active at the chosen temperature.
 118. The methodaccording to claim 117, wherein the length of the single-strandedportion of the partially double-stranded oligonucleotide is between 2and 15 bases.
 119. The method according to claim 118, wherein the lengthof the single-stranded portion of the partially double-strandedoligonucleotide is between 7 and 10 bases.
 120. The method according toclaim 117, wherein the length of the double-stranded portion of thepartially double-stranded oligonucleotide is between 12 and 100 basepairs.
 121. The method according to claim 120, wherein the length of thedouble-stranded portion of the partially double-stranded oligonucleotideis between 20 and 100 base pairs.
 122. A method for preparing a librarycomprising a collection of genetic packages that display a member of adiverse family of peptides, polypeptides or proteins and thatcollectively display at least a portion of the family comprising thesteps: (i) preparing a collection of nucleic acids that code at least inpart for members of the diverse family; (ii) rendering the nucleic acidssingle-stranded; (iii) cleaving the single-stranded nucleic acids at adesired location by a method comprising the steps of: (a) contacting thenucleic acid with a single-stranded oligonucleotide, the oligonucleotidebeing functionally complementary to the nucleic acid in the region inwhich cleavage is desired and including a sequence that with itscomplement in, the nucleic acid forms a restriction endonucleaserecognition site that on restriction results in cleavage of the nucleicacid at the desired location; and (b) cleaving the nucleic acid solelyat the recognition site formed by the complementation of the nucleicacid and the oligonucleotide; the contacting and the cleaving stepsbeing performed at a temperature sufficient to maintain the nucleic acidin substantially single-stranded form, the oligonucleotide beingfunctionally complementary to the nucleic acid over a large enoughregion to allow the two strands to associate such that cleavage mayoccur at the chosen temperature and at the desired location, and thecleavage being carried out using a restriction endonuclease that isactive at the chosen temperature; (iv) contacting the nucleic acid witha partially double-stranded oligonucleotide, the singles stranded regionof the oligonucleotide being functionally complementary to the nucleicacids in the region that remains after the cleavage in step (iii) hasbeen effected, and the double-stranded region of the oligonucleotideincluding any sequences necessary to return the sequences that remainafter cleavage into proper and original reading frame for display andcontaining a restriction endonuclease recognition site 1 of thosesequences that is different from the restriction site used in step(iii); and (v) cleaving the nucleic acid solely at the restrictionendonuclease recognition cleavage site contained within the,double-stranded region of the partially double-stranded oligonucleotide;the contacting and the cleaving steps being performed at a temperaturesufficient to maintain the nucleic acid in substantially single-strandedform, the oligonucleotide being functionally complementary to thenucleic acid over a large enough region to allow the two strands toassociate such that cleavage may occur at the chosen temperature and atthe desired location, and the restriction being carried out using acleavage endonuclease that is active at the chosen temperature; and (vi)displaying a member of the family of peptides, polypeptides or proteinscoded, at least in part, by the cleaved nucleic acids on the surface ofthe genetic package and collectively displaying at least a portion ofthe diversity of the family.
 123. A method for preparing a librarycomprising a collection of members of a diverse family of peptides,polypeptides or proteins and collectively comprising at least a portionof the family comprising the steps: (i) preparing a collection ofnucleic acids that code at least in part for members of the diversefamily; (ii) rendering the nucleic acids single-stranded; (iii) cleavingthe single-stranded nucleic acids at a desired location by a methodcomprising the steps of: (a) contacting the nucleic acid with asingle-stranded oligonucleotide, the oligonucleotide being functionallycomplementary to the nucleic acid in the region in which cleavage isdesired and including a sequence that with its complement in the nucleicacid forms a restriction endonuclease recognition site that onrestriction results in cleavage of the nucleic acid at the desiredlocation; and (b) cleaving the nucleic acid solely at the recognitionsite formed by the complementation of the nucleic acid and theoligonucleotide; the contacting and the cleaving steps being performedat a temperature sufficient to maintain the nucleic acid insubstantially single-stranded form, the oligonucleotide beingfunctionally complementary to the nucleic acid over a large enoughregion to allow the two strands to associate such that cleavage mayoccur at the chosen temperature and at the desired location, and thecleavage being carried out using a restriction endonuclease that isactive at the chosen temperature; (iv) contacting the nucleic acid witha partially double-stranded oligonucleotide, the single-stranded regionof the oligonucleotide being functionally complementary to the nucleicacids in the region that remains after the cleavage in step (iii) hasbeen effected, and the double-stranded region of the oligonucleotideincluding any sequence necessary to return the sequences that remainafter cleavage into proper and original reading frame for expression andcontaining a restriction endonuclease recognition site 5′ of thosesequences that is different from the restriction site used in step(iii); and (v) cleaving the nucleic acid solely at the restrictionendonuclease recognition cleavage site contained within thedouble-stranded region of the partially double-stranded oligonucleotide;the contacting and the cleaving steps being performed at a temperaturesufficient to maintain the nucleic acid in substantially single-strandedform, the oligonucleotide being functionally complementary to thenucleic acid over a large enough region to allow the two strands toassociate such that cleavage may occur at the chosen temperature and atthe desired location, and the restriction being carried out using acleavage endonuclease that is active at the chosen temperature; and (vi)expressing a member of the family of peptides, polypeptides or proteinscoded, at least in part, by the cleaved nucleic acids and collectivelyexpressing at least a portion of the diversity of the family.
 124. Themethod according to claim 122, further comprising at least one nucleicacid amplification step between one or more of steps (i) and (iii) steps(ii) and (iii), steps (iii) and (iv) and steps (iv) and (v).
 125. Alibrary comprising a collection of genetic packages that display amember of a diverse family of peptides, polypeptides or proteins andcollectively display at least a portion of the diversity of the family,the library being produced using the method of claim
 122. 126. A librarycomprising a collection of members of a diverse family of peptides,polypeptides or proteins and collectively comprise at least a portion ofthe diversity of the family, the library being produced using the methodof claim
 123. 127. The method or library according to claim 122, whereinthe members of the library encode an immunoglobulin.
 128. The method orlibrary according to claim 127, wherein the double-stranded region ofthe oligonucleotide encodes at least a part of a framework sequence ofan immunoglobulin.
 129. The method or library according to claim 128,wherein the framework sequence comprises framework 1 of an antibody.130. The method or library according to claim 129, wherein the frameworksequence comprises framework 1 of a variable domain of a light chain.131. The method or library according to claim 129, wherein the frameworksequence comprises framework 1 of a variable domain of a heavy chain.132. A method for displaying a member of a diverse family of peptides,polypeptides or proteins on the surface of a genetic package andcollectively displaying at least a portion of the diversity of thefamily, the method comprising the steps of: (i) preparing a collectionof nucleic acids that code, at least in part, for members of the diversefamily; (ii) rendering the nucleic acids single-stranded; (iii) cleavingthe single-stranded nucleic acids at a desired location by a methodcomprising the steps of: (a) contacting the nucleic acid with apartially double-stranded oligonucleotide, the single-stranded region ofthe oligonucleotide being functionally complementary to the nucleic acidat its 5′ terminal region; and (b) cleaving the nucleic acid solely at arestriction endonuclease cleavage site located in the double-strandedregion of the oligonucleotide or amplifying the nucleic acid using aprimer at least in part functionally complementary to at least a part ofthe double-stranded region of the oligonucleotide, the primer alsointroducing on amplification an endonuclease cleavage site and cleavingthe amplified nucleic acid sequence solely at that site; the contactingand the cleaving steps being performed at a temperature sufficient tomaintain the nucleic acid in substantially single-stranded form, theoligonucleotide being functionally complementary to the nucleic acidover a large enough region to allow the two strands to associate suchthat cleavage may occur at the chosen temperature and at the desiredlocation, and the restriction being carried out using a cleavageendonuclease that is active at the chosen temperature; and (iv)displaying a member of the family of peptides, polypeptides or proteinscoded, at least in part, by the cleaved nucleic acids on the surface ofthe genetic package and collectively displaying at least a portion ofthe diversity of the family.
 133. A method for expressing a member of adiverse family of peptides, polypeptides or proteins and collectivelyexpressing at least a portion of the diversity of the family, the methodcomprising the steps of: (i) preparing a collection of nucleic acidsthat code, at least in part, for members of the diverse family; (ii)rendering the nucleic acids single-stranded; (iii) cleaving thesingle-stranded nucleic acids at a desired location by a methodcomprising the steps of: (a) contacting the nucleic acid with apartially double-stranded oligonucleotide, the single-stranded region ofthe oligonucleotide being functionally complementary to the nucleic acidat its 5′ terminal region; and (b) cleaving the nucleic acid solely at arestriction endonuclease cleavage site located in the double-strandedregion of the nucleotide; or amplifying the nucleic acid using a primerat least in part functionally complementary to at least a part of thedouble-stranded region of the oligonucleotide, the primer alsointroducing on amplification an endonuclease cleavage site and cleavingthe amplified nucleic acid sequence solely at that site; the contactingand the cleaving steps being performed at a temperature sufficient tomaintain the nucleic acid in substantially single-stranded form, theoligonucleotide being functionally complementary to the nucleic acidover a large enough region to allow the two strands to associate suchthat cleavage may occur at the chosen temperature and at the desiredlocation, and the restriction being carried out using a cleavageendonuclease that is active at the chosen temperature; and (iv)expressing a member of the family of peptides, polypeptides or proteinscoded, at least in part, by the cleaved nucleic acids and collectivelyexpressing at least a portion of the diversity of the family.
 134. Themethod according to claim 132, further comprising at least one nucleicacid amplification step between one or more of steps (i) and (ii), steps(ii) and (iii), and steps (iii) and (iv).
 135. A library comprising acollection of genetic packages that display a member of a diverse familyof peptides, polypeptides or proteins and collectively display at leasta portion of the diversity of the family, the library being producedusing the method of claim
 132. 136. A library comprising a collection ofmembers of a diverse family of peptides, polypeptides or proteins andcollectively comprise at least a portion of the diversity of the family,the library being produced using the method of claim
 133. 137. Themethod according to claim 132, wherein the members of the library encodeimmunoglobulins.
 138. A method for cleaving a nucleic acid sequence at adesired location, the method comprising the steps of: (i) contacting asingle-stranded nucleic acid sequence with a partially double-strandedoligonucleotide, the single-stranded region of the oligonucleotide beingfunctionally complementary to the 5′ terminal region of the nucleic acidsequence, the double-stranded region of the oligonucleotide includingany sequences necessary to return the sequence in the single-strandednucleic acid sequence into proper and original reading frame forexpression; and (ii) cleaving the partially double-strandedoligonucleotide-single-stranded nucleic acid combination solely at arestriction endonuclease cleavage site contained within thedouble-stranded oligonucleotide or amplifying the combination using aprimer at least in part functionally complementary to at least part ofthe double-stranded region of the oligonucleotide, the primerintroducing during amplification an endonuclease cleavage site andcleaving the amplified sequence solely at the site.
 139. The methodaccording to claim 138, wherein the length of the single-strandedportion of the partially double-stranded oligonucleotide is between 2and 15 bases.
 140. The method according to claim 139, wherein the lengthof the single-stranded portion of the partially double-strandedoligonucleotide is between 7 and 10 bases.
 141. The method according toclaim 138, wherein the length of the double-stranded portion of thepartially double-stranded oligonucleotide is between 12 and 100 basepairs.
 142. The method according to claim 141, wherein the length of thedouble-stranded portion of the partially double-stranded oligonucleotideis between 20 and 100 base pairs.
 143. The method according to claim138, further comprising at least one nucleic acid amplification stepbetween steps (i) and (ii).